File Changes for mspeir

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

• src/hg/htdocs/FAQ/FAQblat.html
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    09360ed5d9de0f031b6f62924852b533c8fda23a Sat Sep 26 18:45:33 2026 -0700
    Fixing typo in zip name, no refs
• src/hg/htdocs/FAQ/FAQdownloads.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/FAQ/FAQregulation.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    5fd99d465a31d5bd38320ac85ff1969ab9515014 Wed Sep 23 15:44:06 2026 -0700
    Regulation FAQ: correct assembly coverage, add variant effect section, refs #24610 Corrections found by checking the page against our own release announcements, which I should have done before the first commit: - ENCODE4 Regulation is on mm10 as well as hg38. The track symbol differs by assembly (wgEncodeReg4 on hg38, encode4Reg on mm10), so a search by name missed it. - JASPAR 2026 covers hg38, mm39, danRer11, galGal6, dm6, ce11, ci3 and sacCer3. hg19 and mm10 stop at JASPAR 2024. The page had implied all ten were 2026. Also notes that the track holds several releases as subtracks, so the version depends on which one is turned on. - TFBS Conserved is on hg17 as well as hg18 and hg19. - ENCODE4 replaced ENCODE3 as the default in July 2026 and ENCODE3 is kept for archival use. Said in the text and marked in the summary table. - The cell type section described the old subtrack list for the large collections, which now use the faceted interface. - Dropped "composite" and "superTrack", which users should not see. New section on what a single variant does to regulation, covering MPRAVarDB for variants that were actually tested in a reporter assay, and AlphaGenome and PromoterAI for predictions. These live under Phenotype and Disease Associations rather than Regulation, which is worth saying since that is where a reader would otherwise fail to find them. Links to goldenPath/help/hgRegMotifHelp.html from the motif definition and from the JASPAR entry, and the definition now matches the wording there. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    4fa04b06c8c9e1627bb6bedef9e78a02fc4ceb60 Sat Sep 26 16:25:41 2026 -0700
    minor tewaks to wording; removing oreganno refs; removing params from hgTracks links so they use users cart, refs #24610
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    9687a91909838021ee4ca314e2a29c0cccd845c8 Sat Sep 26 16:32:35 2026 -0700
    commenting out the section about loading ENCODE files as CTs, refs #24610
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    3814d8eec23ed1c9f539f669383099eb605dbbcd Sat Sep 26 18:18:00 2026 -0700
    Regulation FAQ: link hgCustom as well as the custom track help, refs #24610
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    b3aef6de6abdf2356bf7d4a64fd5d857726eea6b Sun Oct 4 09:57:49 2026 -0700
    Regulation FAQ: cis-regulation background and six interpretive questions Max asked for a short introduction to cis-regulation, and Lou noted that the page leaned towards listing datasets rather than explaining how to read them. This covers both. A new opening question walks through the kinds of evidence the Browser carries for regulation: open chromatin, histone marks, DNA methylation, transcription factor binding, conservation and physical contact. It is adapted from Max's draft, trimmed where it repeated the sections below it. The top of the page now says when the track list was last checked, and CADD 1.7 goes ahead of AlphaGenome among the variant scores, since it has been stable for years. Six questions are new, each one chosen because people keep asking it on the genome list: why a motif turns up across a whole gene, what a GeneHancer arc does and does not claim, what the scores and grey shading mean (which differs from track to track), whether signal heights can be compared (ENCODE4 auto-scales and ENCODE3 does not, which nothing else documents), what an empty region means, and what to do when your tissue was never assayed. The three "Which tracks show ..." headings become "How do I find ...", which is the form the other FAQ pages use. The Single-cell ATAC-seq row leaves the summary table because singleCellSignalsPeaks is still release alpha and those links error anywhere but hgwdev; the row is kept in a comment to restore when the track is released. refs #24610 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/FAQ/index.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    4d3e56eaa15bfc5d19ee528c03777244d9e1033b Thu Oct 1 15:27:35 2026 -0700
    Add a mailing list search box to the FAQ and Search page The page already linked to the genome mailing list archive, but a link out to Google Groups is easy to miss next to the four search boxes in the same column, and you still have to start the search once you get there. This adds a box alongside the others that hands the query to the group's own search. refs #38438 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/api.html
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    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 252, context: html, text, full: html, text
    a8900aeeb2ac10fba9a4c772f270d15c54279b87 Sat Sep 26 18:55:12 2026 -0700
    rewrite the example assembly hub sections around GenArk instead of genome-test, refs #37641
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    215d7a575ff21f96f5bf8d3d4a3d20f95bd1d95a Sat Sep 26 19:57:36 2026 -0700
    assembly hub docs: fix broken twoBit and BLAT examples, correct mirror IPs, lead with the short hub URL, document hubCheck, refs #37641
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    63c0f6234dbcc0c3fdc9bc2d0e673c8313bd6443 Sun Sep 27 11:57:25 2026 -0700
    two minor fixes from automated CR, #37641
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 94, context: html, text, full: html, text
    2353ec21c6649e1de33b43bd1b3b304603ac71f1 Thu Oct 1 15:31:50 2026 -0700
    Document how to set the order of the bars on a barChart track, refs #37619 Adds a "Setting the order of the bars" section to the barChart format page. It explains that the order is a property of the data file rather than of the display, that barChartBars, barChartCategoryUrl, barChartColors and the barChartStatsUrl rows are all positional and have to move together, and then gives three recipes: barChartReorder on a barChart file, the same wrapped in bigBedToBed and bedToBigBed for a bigBarChart, and expMatrixToBarchartBed --groupOrderFile for anyone who is still at the matrix stage and can get the order right the first time. The barChartBars entry in trackDbLibrary.shtml gains a line saying the labels are positional, with a link to the new section. Also corrects the bedToBigBed command in Example 4 to pass -sort. expMatrixToBarchartBed writes its rows in item-name order, since it joins on name, so bedToBigBed rejects the file as unsorted as soon as the two orders disagree. The example has always worked on the three-row file we host, whose rows happen to be in position order already, and fails on real data. Checked the claims against the code rather than against the existing prose: barChartTrack.c walks expScores and the category list in step at increasing x with no sort anywhere, createCategs numbers the categories in label order, facetedTableSelectOffsets hands back the stats row index as the expScores offset, and getSampleValsFromFile matches samples to categories by name, which is why the matrix and sample files need no changes. Every command and both example orderings were run against the files already published under goldenPath/help/examples/barChart. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/bigPsl.html
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    4d43b746e730f4cf9df40e70d715e75b33ed6fca Tue Sep 22 14:43:59 2026 -0700
    Explain the bigPsl o-prefixed field names on the help page, refs #37155 The autoSql field comments now name the PSL field each o-prefixed field corresponds to, but nothing on the page said what the o fields are or why they are named after chromosomes when the aligned sequence is usually a transcript or protein. Add a paragraph under the schema block. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 6, context: html, text, full: html, text
    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 3, context: html, text, full: html, text
    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    a8900aeeb2ac10fba9a4c772f270d15c54279b87 Sat Sep 26 18:55:12 2026 -0700
    rewrite the example assembly hub sections around GenArk instead of genome-test, refs #37641
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    215d7a575ff21f96f5bf8d3d4a3d20f95bd1d95a Sat Sep 26 19:57:36 2026 -0700
    assembly hub docs: fix broken twoBit and BLAT examples, correct mirror IPs, lead with the short hub URL, document hubCheck, refs #37641
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    2353ec21c6649e1de33b43bd1b3b304603ac71f1 Thu Oct 1 15:31:50 2026 -0700
    Document how to set the order of the bars on a barChart track, refs #37619 Adds a "Setting the order of the bars" section to the barChart format page. It explains that the order is a property of the data file rather than of the display, that barChartBars, barChartCategoryUrl, barChartColors and the barChartStatsUrl rows are all positional and have to move together, and then gives three recipes: barChartReorder on a barChart file, the same wrapped in bigBedToBed and bedToBigBed for a bigBarChart, and expMatrixToBarchartBed --groupOrderFile for anyone who is still at the matrix stage and can get the order right the first time. The barChartBars entry in trackDbLibrary.shtml gains a line saying the labels are positional, with a link to the new section. Also corrects the bedToBigBed command in Example 4 to pass -sort. expMatrixToBarchartBed writes its rows in item-name order, since it joins on name, so bedToBigBed rejects the file as unsorted as soon as the two orders disagree. The example has always worked on the three-row file we host, whose rows happen to be in position order already, and fails on real data. Checked the claims against the code rather than against the existing prose: barChartTrack.c walks expScores and the category list in step at increasing x with no sort anywhere, createCategs numbers the categories in label order, facetedTableSelectOffsets hands back the stats row index as the expScores offset, and getSampleValsFromFile matches samples to categories by name, which is why the matrix and sample files need no changes. Every command and both example orderings were run against the files already published under goldenPath/help/examples/barChart. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/dataApi.html
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    1225a489c7de73798ed0051d2141d876a3969486 Sat Sep 26 18:55:01 2026 -0700
    remove orphaned inc/dataApi.html, superseded by goldenPath/help/api.html, refs #37641
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal3/phastConsElements7way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chimp/panTro2/multiz8way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cow/bosTau4/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/dog/canFam2/phastConsElements4way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements15way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm3/phastConsElements15way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/horse/equCab2/phastConsElements6way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/chm13/html/GCA_009914755.4_T2T-CHM13v2.0.hgLiftOver.html
  • lines changed 2, context: html, text, full: html, text
    733c551e32c88c02773c20af61169100edfb446a Sun Sep 27 16:00:39 2026 -0700
    CHM13 liftOver examples: point at public hs1 instead of a genome-test hub id, refs #37641
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg17/multiz8way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg17/phastConsElements17way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multiz17way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 31, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 10, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phastConsElements17way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 34, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    b9c41cec68f33aec1a64d8cc709af9afc15155fa Fri Sep 25 22:49:03 2026 -0700
    hg38 cons241way: point the phyloP tree model text at the directory, refs #34803 The link went to phyloP241way/hg38.phyloP241way.mod, which does not exist and never has under that name. The models live in cactus241way/phyloP241way, and there are three of them rather than one: a general model and separate chrX and chrY models. Link the directory and say so. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons27way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 45, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lamprey/petMar1/phastConsElements6way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lancelet/braFlo1/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 40, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat1/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
  • lines changed 25, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm5/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm6/multiz10way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 31, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/phastConsElements17way.html
  • lines changed 8, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/multiz5way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 8, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn4/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rhesus/rheMac2/multiz5waySyn.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • lines changed 37, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 38, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/stickleback/gasAcu1/phastConsElements8way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 39, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
  • lines changed 48, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro2/phastConsElements7way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 37, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/barChartReorder
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/makefile
  • lines changed 11, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/bars.txt
  • lines changed 1, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/simple.bed
  • lines changed 2, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/test.bed
  • lines changed 4, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/test.categories
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/bad.newOrder
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/short.bed
  • lines changed 1, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/simple.bed
  • lines changed 2, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.bed
  • lines changed 4, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.categories
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.newOrder
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.oldOrder
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/makefile
  • lines changed 35, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/allOptions.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/allOptions2.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/extraFields.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/floats.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/test.output
  • lines changed 10, context: html, text, full: html, text
    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/test.output2
  • lines changed 10, context: html, text, full: html, text
    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/makefile
  • lines changed 4, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/userApps/mkREADME.sh
  • lines changed 1, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>