All File Changes

v500_base to v501_preview (2026-06-29 to 2026-07-06) v501

• confs/asia.hg.conf
  • lines changed 8, context: html, text, full: html, text
    4e743e62e2c8ffdf81d57f7fec38f3598b866bc2 Sun Jul 5 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 8, context: html, text, full: html, text
    4e743e62e2c8ffdf81d57f7fec38f3598b866bc2 Sun Jul 5 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 5, context: html, text, full: html, text
    4e743e62e2c8ffdf81d57f7fec38f3598b866bc2 Sun Jul 5 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 5, context: html, text, full: html, text
    4e743e62e2c8ffdf81d57f7fec38f3598b866bc2 Sun Jul 5 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/file-formats/autoSql.md
  • lines changed 266, context: html, text, full: html, text
    31b48d9f3e1de4925f46aebd940f46828a5d7af6 Sun Jul 5 11:20:15 2026 -0700
    new page describing autoSql format, refs #37537
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 5, context: html, text, full: html, text
    954df0aeb6614b0f438e2888d247eaceac8340cc Wed Jul 1 10:53:10 2026 -0700
    Adding Broads revised Y5 Aims3/4 (columnF, row 13,14,17)
• src/hg/hgBlat/hgBlat.c
  • lines changed 10, context: html, text, full: html, text
    099dda2013e7caffde097371fa68de467a2c5085 Tue Jun 30 05:14:13 2026 -0700
    hgBlat: fix bugs in showAliPlaces BLAT results page - Fix inverted JS test in buildBigPslCt: 'if (!ct_blat !== "")' always evaluated true (a boolean strict-compared to a string), so the remove-custom-track vars were appended on every call. Should be 'if (ct_blat !== "")'. - Escape trackName/trackDescription with javaScriptLiteralEncode before interpolating them into single-quoted JS literals. They derive from the user FASTA header (psl->qName), so a quote broke the script / allowed injection. - Remove a stray re-opened <TT><PRE> in the PSL-output branch that left unbalanced tags. - Free the leaked locusConn connection and subList in the hyperlink branch.
  • lines changed 107, context: html, text, full: html, text
    48cd1865d252867ebbd3852d76bed271d0028d29 Tue Jun 30 05:33:14 2026 -0700
    hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js The "Create a stable custom track" (autoBigPsl) results page emitted ~140 lines of JavaScript as C string literals via jsInlineF/jsInline. Move that code into a real, jshint-clean hgBlat.js and have hgBlat.c emit only a small hgBlatData config object (url, trackName, trackDescription, and the custom-track cart var names) plus a jsIncludeFile("hgBlat.js"). Behavior is unchanged. The track name/description are still javaScriptLiteralEncode'd before interpolation.
  • lines changed 107, context: html, text, full: html, text
    cceb0f154b33d600926d6948c148305625756749 Tue Jun 30 17:35:50 2026 -0700
    Revert "hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js" This reverts commit 48cd1865d252867ebbd3852d76bed271d0028d29.
  • lines changed 10, context: html, text, full: html, text
    18ef76d32c407a89bc0d7d8fd329d735c79eef1a Tue Jun 30 17:35:58 2026 -0700
    Revert "hgBlat: fix bugs in showAliPlaces BLAT results page" This reverts commit 099dda2013e7caffde097371fa68de467a2c5085.
• src/hg/hgConvert/hgConvert.c
  • lines changed 34, context: html, text, full: html, text
    f80b3826a921197488ece1440ff08038ec9e572d Mon Jun 29 12:28:07 2026 -0700
    hgConvert/hgTracks: add option to hide target default tracks on QuickLift convert Adds a "Hide all default tracks on the target" checkbox (on by default) to the Convert page when QuickLift is enabled. When set, the QuickLift link appends hideTracks=on, and hgTracks now leaves QuickLifted tracks visible when hiding the target assembly's default tracks. refs #37815
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 15, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/cds.c
  • lines changed 64, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 134, context: html, text, full: html, text
    ded41ea1968e30e2c248f65d1c9fec9793cb82fc Thu Jun 18 11:31:32 2026 -0700
    hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display When a coding transcript is zoomed in far enough to color its codons, the coding boxes carried no visible strand cue: only the introns showed the barbed "fishbone" arrows, and the strand was otherwise visible only on mouseover. This adds strand-direction chevrons to the codon and UTR display so the reading direction is visible at a glance. - At the amino-acid (codon-text) level, drawScaledBoxWithText() draws a chevron at each codon's left boundary (in the whitespace between the centered letters), in the box's contrasting color (white on the dark-blue codon shades), before the letter so the letter stays crisp. Points right on + strand, left on -; reverse-complement display is handled by hvGfxLine. The base-position ruler's codon display passes strand 0 and is unaffected. - When codons are colored but too small to label, baseColorDrawCdsArrows() distributes white chevrons across the coding part of each exon, on top of the boxes, at twice the standard barb spacing. - The UTRs (which never showed arrows) now get chevrons too, in the feature's contrasting color at a wider (3x) spacing as a cue that they are non-coding. The chevron is sized to the short UTR box, with a 1px floor so it still shows in squish mode. refs #37779
• src/hg/hgTracks/cds.h
  • lines changed 10, context: html, text, full: html, text
    ded41ea1968e30e2c248f65d1c9fec9793cb82fc Thu Jun 18 11:31:32 2026 -0700
    hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display When a coding transcript is zoomed in far enough to color its codons, the coding boxes carried no visible strand cue: only the introns showed the barbed "fishbone" arrows, and the strand was otherwise visible only on mouseover. This adds strand-direction chevrons to the codon and UTR display so the reading direction is visible at a glance. - At the amino-acid (codon-text) level, drawScaledBoxWithText() draws a chevron at each codon's left boundary (in the whitespace between the centered letters), in the box's contrasting color (white on the dark-blue codon shades), before the letter so the letter stays crisp. Points right on + strand, left on -; reverse-complement display is handled by hvGfxLine. The base-position ruler's codon display passes strand 0 and is unaffected. - When codons are colored but too small to label, baseColorDrawCdsArrows() distributes white chevrons across the coding part of each exon, on top of the boxes, at twice the standard barb spacing. - The UTRs (which never showed arrows) now get chevrons too, in the feature's contrasting color at a wider (3x) spacing as a cue that they are non-coding. The chevron is sized to the short UTR box, with a 1px floor so it still shows in squish mode. refs #37779
• src/hg/hgTracks/decorator.c
  • lines changed 33, context: html, text, full: html, text
    43697ed2271f7819ef6d6f1947c0b404a508539a Wed Jul 1 15:38:24 2026 -0700
    Make hgTracks decorators resolve the decoratedItem chrom through chromAlias so decorations link to their items when the decoratedItem field uses an alias (e.g. PanSN or accession names) rather than the native sequence name. refs #37803
• src/hg/hgTracks/hgTracks.c
  • lines changed 0, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    d806d4e2ec73a0e53f8b65443bb5a403cc54364d Mon Jun 29 12:11:00 2026 -0700
    Enable Sort by Magnitude/Similarity on wiggle-only composites, refs #37816 The right-click "Sort by Magnitude/Similarity" menu items were previously offered only on custom composites. Extend them to any composite whose subtracks are all wiggle types (parentIsAllWiggle in utils.js).
  • lines changed 9, context: html, text, full: html, text
    f80b3826a921197488ece1440ff08038ec9e572d Mon Jun 29 12:28:07 2026 -0700
    hgConvert/hgTracks: add option to hide target default tracks on QuickLift convert Adds a "Hide all default tracks on the target" checkbox (on by default) to the Convert page when QuickLift is enabled. When set, the QuickLift link appends hideTracks=on, and hgTracks now leaves QuickLifted tracks visible when hiding the target assembly's default tracks. refs #37815
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/simpleTracks.c
  • lines changed 29, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    ded41ea1968e30e2c248f65d1c9fec9793cb82fc Thu Jun 18 11:31:32 2026 -0700
    hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display When a coding transcript is zoomed in far enough to color its codons, the coding boxes carried no visible strand cue: only the introns showed the barbed "fishbone" arrows, and the strand was otherwise visible only on mouseover. This adds strand-direction chevrons to the codon and UTR display so the reading direction is visible at a glance. - At the amino-acid (codon-text) level, drawScaledBoxWithText() draws a chevron at each codon's left boundary (in the whitespace between the centered letters), in the box's contrasting color (white on the dark-blue codon shades), before the letter so the letter stays crisp. Points right on + strand, left on -; reverse-complement display is handled by hvGfxLine. The base-position ruler's codon display passes strand 0 and is unaffected. - When codons are colored but too small to label, baseColorDrawCdsArrows() distributes white chevrons across the coding part of each exon, on top of the boxes, at twice the standard barb spacing. - The UTRs (which never showed arrows) now get chevrons too, in the feature's contrasting color at a wider (3x) spacing as a cue that they are non-coding. The chevron is sized to the short UTR box, with a 1px floor so it still shows in squish mode. refs #37779
  • lines changed 2, context: html, text, full: html, text
    0b75f5aba4e7dbf1389993bbdba8547b0bb428c3 Tue Jun 30 02:59:45 2026 -0700
    change strand back to single character, refs #37779
• src/hg/hgTracks/sortWig.c
  • lines changed 5, context: html, text, full: html, text
    d806d4e2ec73a0e53f8b65443bb5a403cc54364d Mon Jun 29 12:11:00 2026 -0700
    Enable Sort by Magnitude/Similarity on wiggle-only composites, refs #37816 The right-click "Sort by Magnitude/Similarity" menu items were previously offered only on custom composites. Extend them to any composite whose subtracks are all wiggle types (parentIsAllWiggle in utils.js).
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 2, context: html, text, full: html, text
    01b4de30d4b9c4f44780dee46e1cadb65b23b126 Sun Jul 5 11:26:05 2026 -0700
    Adding link to new AutoSql doc, refs #37537
  • lines changed 1, context: html, text, full: html, text
    815537305c3d65e046b8de189c89622be82d121b Sun Jul 5 11:30:06 2026 -0700
    tweaking AutoSql link label, refs #37537
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 100, context: html, text, full: html, text
    aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
    varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026".
  • lines changed 16, context: html, text, full: html, text
    30c0e2e97dc0f5391a58a3cc665f55697a3b6152 Tue Jun 30 18:03:44 2026 -0700
    varFreqs: newsarch, swap "supertrack" for "container track" and expand credits. refs #36642 Per Max's post-release feedback on the ticket: "supertrack" is jargon for end users, so all 4 mentions in the SNV Frequencies entry are swapped to "container track". Credits paragraph expanded to name the additional investigators and data-access teams who provided source variant files or helped shape the track (Sarah Tishkoff, Yanan Cao, Matthew Hobbs, Adam Ameur, Johan Viklund, Ameena Suliman, Julia Sommer, Cole Shanks, Qudsi Aljabiri). Also fixes "Insoo Jang" spelling to "Insu Jang" to match his own signature.
• src/hg/htdocs/images/snvFrequenciesNewsarch.png
  • lines changed 0, context: html, text, full: html, text
    aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
    varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026".
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
    varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026".
• src/hg/hubApi/liftOver.c
  • lines changed 6, context: html, text, full: html, text
    1948a03c367e4a9686f0bda2a6427859e3f4138a Wed Jul 1 12:10:01 2026 -0700
    do not talk to ottoTable until you really need to do that - patch fix for v500 refs #37839
  • lines changed 4, context: html, text, full: html, text
    4b3e6dfbb1b3a575a01e6f9915db026d356c6251 Wed Jul 1 17:17:29 2026 -0700
    and can check ottoTable exists before making central connection refs #37839
• src/hg/js/hgBlat.js
  • lines changed 74, context: html, text, full: html, text
    48cd1865d252867ebbd3852d76bed271d0028d29 Tue Jun 30 05:33:14 2026 -0700
    hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js The "Create a stable custom track" (autoBigPsl) results page emitted ~140 lines of JavaScript as C string literals via jsInlineF/jsInline. Move that code into a real, jshint-clean hgBlat.js and have hgBlat.c emit only a small hgBlatData config object (url, trackName, trackDescription, and the custom-track cart var names) plus a jsIncludeFile("hgBlat.js"). Behavior is unchanged. The track name/description are still javaScriptLiteralEncode'd before interpolation.
  • lines changed 74, context: html, text, full: html, text
    cceb0f154b33d600926d6948c148305625756749 Tue Jun 30 17:35:50 2026 -0700
    Revert "hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js" This reverts commit 48cd1865d252867ebbd3852d76bed271d0028d29.
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    d806d4e2ec73a0e53f8b65443bb5a403cc54364d Mon Jun 29 12:11:00 2026 -0700
    Enable Sort by Magnitude/Similarity on wiggle-only composites, refs #37816 The right-click "Sort by Magnitude/Similarity" menu items were previously offered only on custom composites. Extend them to any composite whose subtracks are all wiggle types (parentIsAllWiggle in utils.js).
  • lines changed 2, context: html, text, full: html, text
    e6a7d9a7a4652ed62ef66c1df82e5962dc74c18f Tue Jun 30 14:58:14 2026 -0700
    Fix shift+drag on ruler to show the zoom/highlight dialog again, refs #27113 Commit 36b9de7c24c made a single click on the ruler always zoom by adding "&& !rulerClicked" to the dialog-gating condition in selectEnd. But rulerClicked only means the gesture started in the ruler band, not that it was a click, so it also routed ruler shift+drags straight to zoom instead of opening the dialog. Gate on "!(rulerClicked && singleClick)" so only a genuine single click on the ruler skips the dialog; a drag-select on the ruler shows it as before.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    48cd1865d252867ebbd3852d76bed271d0028d29 Tue Jun 30 05:33:14 2026 -0700
    hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js The "Create a stable custom track" (autoBigPsl) results page emitted ~140 lines of JavaScript as C string literals via jsInlineF/jsInline. Move that code into a real, jshint-clean hgBlat.js and have hgBlat.c emit only a small hgBlatData config object (url, trackName, trackDescription, and the custom-track cart var names) plus a jsIncludeFile("hgBlat.js"). Behavior is unchanged. The track name/description are still javaScriptLiteralEncode'd before interpolation.
  • lines changed 1, context: html, text, full: html, text
    cceb0f154b33d600926d6948c148305625756749 Tue Jun 30 17:35:50 2026 -0700
    Revert "hgBlat: move showAliPlaces autoBigPsl inline JS into src/hg/js/hgBlat.js" This reverts commit 48cd1865d252867ebbd3852d76bed271d0028d29.
• src/hg/js/utils.js
  • lines changed 16, context: html, text, full: html, text
    d806d4e2ec73a0e53f8b65443bb5a403cc54364d Mon Jun 29 12:11:00 2026 -0700
    Enable Sort by Magnitude/Similarity on wiggle-only composites, refs #37816 The right-click "Sort by Magnitude/Similarity" menu items were previously offered only on custom composites. Extend them to any composite whose subtracks are all wiggle types (parentIsAllWiggle in utils.js).
• src/hg/lib/cart.c
  • lines changed 15, context: html, text, full: html, text
    214e76748ab09f24db9e390c633482be7901e8ab Tue Jun 30 16:58:26 2026 -0700
    adding captcha tracing to cart.c, no redmine
• src/hg/makeDb/doc/Cardiomyopathy.txt
  • lines changed 502, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/doc/hg38/popEve.txt
  • lines changed 79, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 57, context: html, text, full: html, text
    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAFfrequencies.py
  • lines changed 253, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
  • lines changed 189, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAtlasEF.py
  • lines changed 460, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPCardioBoost.py
  • lines changed 136, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinDomains.py
  • lines changed 339, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinVar506161.py
  • lines changed 275, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPEvRepo.py
  • lines changed 396, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPPVS1.py
  • lines changed 217, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
  • lines changed 554, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPRevel.py
  • lines changed 188, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py
  • lines changed 354, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalshOR.py
  • lines changed 180, context: html, text, full: html, text
    aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700
    Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
  • lines changed 1, context: html, text, full: html, text
    fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
    lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
• src/hg/makeDb/scripts/popEve/extractPopEve.py
  • lines changed 99, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/scripts/popEve/popEve_heatmap.as
  • lines changed 24, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py
  • lines changed 268, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/scripts/tad/buildTads3dgb.py
  • lines changed 1, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/scripts/tad/buildTadsEncode.py
  • lines changed 2, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/scripts/varFreqs/databases.tsv
  • lines changed 10, context: html, text, full: html, text
    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
  • lines changed 63, context: html, text, full: html, text
    753697fc7582b1dec5392c3ab1971e8f0f7e8e6f Fri Jun 19 08:58:02 2026 -0700
    varFreqs: fix numeric filter rendering and trim per-cohort filters #Preview2 week - bugs introduced now will need a build patch to fix The Affected/Background track config pages showed none of the AF/AC/AN filters. hgTrackUi only discovers a numeric filter from a filter.<field> (or <field>Filter) setting (FILTER_NUMBER_WILDCARD in bigBedFilter.h); the generated fragment had only filterByRange.<field>/filterLimits.<field> for those fields, so they were silently dropped. vcfToBigBed.py now emits filter.<field> (a full-range default, so nothing is filtered by default) plus filterLimits for every numeric filter. That made ~140 filters appear, which overwhelmed the config page, so the per-database and per-population AF/AC filters are emitted commented out (range_filter enabled=False) and can be re-enabled individually by removing the leading "# ". Only the global filters remain active: variant type, consequence, the affected/case and background AF/AC/AN summaries, the affected/case-cohort and background-source selectors, the in-affected flag, and the length filters. The per-cohort data columns are unchanged in the bigBed and still show on the details page. No bigBed rebuild needed; this is trackDb-only. refs #36642
  • lines changed 95, context: html, text, full: html, text
    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
• src/hg/makeDb/trackDb/betaGenArk.txt
  • lines changed 1, context: html, text, full: html, text
    736542dd619206870dc1e7e826d8a59ceeb3a659 Tue Jun 30 10:52:52 2026 -0700
    starting evaSnp9 refs #37517
• src/hg/makeDb/trackDb/human/aou1kSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/aprSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/chirmade101Sv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/colorsDbSv.html
  • lines changed 8, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/cpc1Sv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/decodeSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
  • lines changed 4, context: html, text, full: html, text
    fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
    lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
• src/hg/makeDb/trackDb/human/ga4kSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/gustafsonSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/han945Sv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/hg19/tad.ra
  • lines changed 24, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hg19/tads.html
  • lines changed 23, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hg38/tad.ra
  • lines changed 24, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hg38/tads.html
  • lines changed 25, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra
  • lines changed 464, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra
  • lines changed 117, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/human/hgsvc2Sv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/hgsvc3Sv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/hprc2v21Sv.html
  • lines changed 2, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/hs1/hgLiftOver.trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    da07f42778c2e7fa01915f8bae62e0ff3bc1bbe1 Sun Jul 5 17:52:03 2026 -0700
    Fixing paths for hs1 liftOver track files, refs #36230
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 8, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
  • lines changed 20, context: html, text, full: html, text
    fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
    lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
• src/hg/makeDb/trackDb/human/lrSv.ra
  • lines changed 17, context: html, text, full: html, text
    fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
    lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
• src/hg/makeDb/trackDb/human/lrSv1kgOnt.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/lrSvAll.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/lrSvAll.ra
  • lines changed 1, context: html, text, full: html, text
    fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700
    lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
• src/hg/makeDb/trackDb/human/popEve.html
  • lines changed 181, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/trackDb/human/popEve.ra
  • lines changed 13, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 43, context: html, text, full: html, text
    10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8 Tue Jun 30 17:57:33 2026 -0700
    Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791 Document EVE and popEVE on the predictionScoresSuper description page, which previously listed the other member scores but not these two. Also add reciprocal relatedTracks cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700
    Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
• src/hg/makeDb/trackDb/human/tommoJpSv.html
  • lines changed 1, context: html, text, full: html, text
    9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700
    lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 1098, context: html, text, full: html, text
    753697fc7582b1dec5392c3ab1971e8f0f7e8e6f Fri Jun 19 08:58:02 2026 -0700
    varFreqs: fix numeric filter rendering and trim per-cohort filters #Preview2 week - bugs introduced now will need a build patch to fix The Affected/Background track config pages showed none of the AF/AC/AN filters. hgTrackUi only discovers a numeric filter from a filter.<field> (or <field>Filter) setting (FILTER_NUMBER_WILDCARD in bigBedFilter.h); the generated fragment had only filterByRange.<field>/filterLimits.<field> for those fields, so they were silently dropped. vcfToBigBed.py now emits filter.<field> (a full-range default, so nothing is filtered by default) plus filterLimits for every numeric filter. That made ~140 filters appear, which overwhelmed the config page, so the per-database and per-population AF/AC filters are emitted commented out (range_filter enabled=False) and can be re-enabled individually by removing the leading "# ". Only the global filters remain active: variant type, consequence, the affected/case and background AF/AC/AN summaries, the affected/case-cohort and background-source selectors, the in-affected flag, and the length filters. The per-cohort data columns are unchanged in the bigBed and still show on the details page. No bigBed rebuild needed; this is trackDb-only. refs #36642
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    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
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    aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700
    varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026".
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
  • lines changed 15, context: html, text, full: html, text
    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
  • lines changed 29, context: html, text, full: html, text
    5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700
    varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
• src/hg/makeDb/trackDb/mouse/mm10/tad.ra
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    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm10/tads.html
  • lines changed 22, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra
  • lines changed 30, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra
  • lines changed 16, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm39/tad.ra
  • lines changed 2, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm39/tads.html
  • lines changed 22, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
  • lines changed 30, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra
  • lines changed 16, context: html, text, full: html, text
    5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700
    Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
• src/hg/makeDb/trackDb/relatedTracks.ra
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    10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8 Tue Jun 30 17:57:33 2026 -0700
    Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791 Document EVE and popEVE on the predictionScoresSuper description page, which previously listed the other member scores but not these two. Also add reciprocal relatedTracks cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.
• src/hg/utils/otto/g2p/README.md
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    ba5350e41c26185f48dd56d074219d3a2eab7aed Thu Jul 2 10:32:20 2026 -0700
    New otto framework for G2P track, refs #36736
• src/hg/utils/otto/g2p/doG2p.py
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    ba5350e41c26185f48dd56d074219d3a2eab7aed Thu Jul 2 10:32:20 2026 -0700
    New otto framework for G2P track, refs #36736
• src/hg/utils/otto/g2p/expectedColumns.txt
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    ba5350e41c26185f48dd56d074219d3a2eab7aed Thu Jul 2 10:32:20 2026 -0700
    New otto framework for G2P track, refs #36736
• src/hg/utils/otto/g2p/g2p.as
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    ba5350e41c26185f48dd56d074219d3a2eab7aed Thu Jul 2 10:32:20 2026 -0700
    New otto framework for G2P track, refs #36736
• src/hg/utils/otto/g2p/g2pWrapper.sh
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    ba5350e41c26185f48dd56d074219d3a2eab7aed Thu Jul 2 10:32:20 2026 -0700
    New otto framework for G2P track, refs #36736
• src/hg/utils/otto/otto.crontab
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    696ce0adb22c81b1df4f2a83efe46a4d987d23c9 Thu Jul 2 14:11:45 2026 -0700
    Updating source tree crontab for G2P run, refs #36736
• src/hg/utils/otto/panelApp/doPanelApp.py
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    2dda14f9c5394e1d6fa30f3da69e74b8e8b84413 Tue Jun 30 15:34:05 2026 -0700
    Fix panelApp otto crash when reading Ensembl gene locations. The script hardcoded the Ensembl release sub-key (GRch37/82, GRch38/90) when pulling gene coordinates, but PanelApp Australia moved to releases 87/115. Every Australia gene then failed both assembly lookups, leaving the dataframes empty and raising a column-count ValueError. Added an ensemblBuild() helper that selects whichever release key the API returns, and routed all gene/STR coordinate and ensembl_id lookups through it. England (still on 82/90) is unaffected. No RM, refs otto
• src/inc/dnautil.h
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    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/dnautil.c
  • lines changed 14, context: html, text, full: html, text
    6d437c28a5ff82a2af59ca516559053c4bf7c3f9 Thu Jun 18 01:18:34 2026 -0700
    hgTracks: amino-acid name in codon + ruler mouseovers; exon-length label; ruler "Complement bases" config toggle Three genome browser display changes around AA display: 1) amino acids shown on genePred codons and on rule codons, and making the "complement option" easier to find. 1) The genePred/bigGenePred codon mouseover (zoomed to the codon level) now shows the codon's amino acid on its own "Amino acid:" line, as the three-letter abbreviation plus full name (e.g. "Ala (alanine)"). Rather than reverse-decode the amino acid out of the codon's packed grayIx, the one-letter code is now stored on the codon when it is translated: struct simpleFeature gains a codonAa field, codonToGrayIx() reports the letter through a new out-param, and the codon mouseover reads simpleFeature.codonAa directly. The drawn codon letter and the mouseover then derive from the same translation and cannot drift apart, without the mouseover having to understand the grayIx encoding (the drawing path, colorAndCodonFromGrayIx(), still decodes its own grayIx inline, unchanged). Adds a one-letter->full-name aaToName() in lib/dnautil.c (using the previously unused name field of aminoAcidTable). Stop codons show "Ter (termination)". Also relabels the exon "Length" field as "Exon Length" in the codon and zoomed-out exon mouseovers; introns keep "Length". 2) The base-position ruler's three-reading-frame translation (hgt.baseShowCodons) now gives each codon box a mouse-over with the same three-letter abbreviation and full name, reading the stored codonAa via aaToName()/aaToAbbr() (baseColorDrawRulerCodons in cds.c). 3) Adds a "Complement the bases" checkbox to the base position (ruler) track configuration page (hgTrackUi rulerUi). It toggles the same per-assembly COMPLEMENT_BASES_VAR cart variable that was previously reachable only by clicking the "Click to complement" arrow next to the ruler. Also fixes the indentation of the adjacent drawComplementArrow() text assignments. refs #37779 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/pngToLolly/README.md
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    feae7a22b855ea17109a9c99eb95c3369626ff19 Mon Jun 29 14:13:49 2026 -0700
    pngToLolly: new utility to render a PNG as a bigLolly dot-mosaic track Each opaque pixel of the downscaled image becomes one stemless lolly: column -> genomic position, row -> lolly value, pixel color -> itemRgb, and local image detail varies the dot size. Emits a ready-to-build hub plus makeHub.sh. By default writes a self-contained synthetic assembly hub; with -db/-pos it lays the mosaic across a window of an existing assembly as a track hub. Dot sizes use the browser's standard percent-of-height lolly sizing. Adds a README covering usage, options, and the canvas-size/dot-size trade-off.
• src/utils/pngToLolly/makefile
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    feae7a22b855ea17109a9c99eb95c3369626ff19 Mon Jun 29 14:13:49 2026 -0700
    pngToLolly: new utility to render a PNG as a bigLolly dot-mosaic track Each opaque pixel of the downscaled image becomes one stemless lolly: column -> genomic position, row -> lolly value, pixel color -> itemRgb, and local image detail varies the dot size. Emits a ready-to-build hub plus makeHub.sh. By default writes a self-contained synthetic assembly hub; with -db/-pos it lays the mosaic across a window of an existing assembly as a track hub. Dot sizes use the browser's standard percent-of-height lolly sizing. Adds a README covering usage, options, and the canvas-size/dot-size trade-off.
• src/utils/pngToLolly/pngToLolly.c
  • lines changed 545, context: html, text, full: html, text
    feae7a22b855ea17109a9c99eb95c3369626ff19 Mon Jun 29 14:13:49 2026 -0700
    pngToLolly: new utility to render a PNG as a bigLolly dot-mosaic track Each opaque pixel of the downscaled image becomes one stemless lolly: column -> genomic position, row -> lolly value, pixel color -> itemRgb, and local image detail varies the dot size. Emits a ready-to-build hub plus makeHub.sh. By default writes a self-contained synthetic assembly hub; with -db/-pos it lays the mosaic across a window of an existing assembly as a track hub. Dot sizes use the browser's standard percent-of-height lolly sizing. Adds a README covering usage, options, and the canvas-size/dot-size trade-off.
• src/utils/qa/errorLogKeywordSearch.py
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    b761e0e7b483d9fbb2832820c138c0baab13a869 Thu Jul 2 17:39:24 2026 -0700
    Fix Total out of memory metric in errorLogKeywordSearch.py to count only genuine events. refs #37699 A single needMem OOM failure recurses in the errAbort/warn handler (which itself allocates), re-emitting the "request size %llu bytes" format string many times per crash. The old grep "needMem: Out of memory" counted every one of those frames, inflating the weekly count ~60-175x (e.g. ~1070 reported vs ~18 genuine events for the week of 20260614). Restrict the match to lines with a numeric request size so only real allocation failures are counted.
• src/utils/qa/mlqAutomate.py
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    04d357c39c6ba5ec5899b5341803942a75864c26 Mon Jun 29 13:18:17 2026 -0700
    Fix MLQ automation by updating retired Sonnet model ID to claude-sonnet-4-6 and alerting the QA team on non-retryable Claude API errors instead of silently logging them as overloaded. No RM. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/redmineCli
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    4ec511e6d18ea08b0b623cfc9100e193ea167a8a Tue Jun 30 17:18:42 2026 -0700
    redmineCli: add build-patch subcommand for Build Patch tickets, refs #37281 The Build Patch tracker requires five custom fields (Commit ID, Files Changed, CGIs to retest, Test Case, Suggested Code Reviewer), so a plain create returns HTTP 422 and the fields had to be set with a hand-built API POST. The new build-patch subcommand does it in one call: sets the GB project, Build Patch tracker, Urgent priority, New status, and blank assignee; fills the required custom fields plus Developer and an optional Post-mortem; resolves developer, reviewer, and target-version names to IDs; relates the ticket to the bug it fixes; and adds the QA Team and build meister as watchers.

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• files changed: 125