All File Changes

v456_base to v457_preview (2023-10-30 to 2023-11-06) v457

• src/hg/cgilib/cartJson.c
  • lines changed 51, context: html, text, full: html, text
    401691176ea0ade97d1c643bc2ed4c382fee1ef2 Fri Nov 3 16:59:50 2023 -0700
    Fix multi-term searches when using genomePosCJ: 1. make sure to collapse hgps together and combine highlight strings and item highlight names, 2. make sure hgSearch checks the json data returned during its init function if there was an error from the search term, such as different chromosomes for a multi-term search, refs #22978
• src/hg/hgc/hgc.c
  • lines changed 18, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
  • lines changed 5, context: html, text, full: html, text
    dad13f95ddaaa0f9c9b111fdc6454b0a3053c1c0 Tue Oct 31 10:56:18 2023 -0700
    Fix broken tables on hgc pages for tracks with the detailsDynamicTable setting, refs #32269,#32519
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 25, context: html, text, full: html, text
    c7f117d5fc2aee9e65222776a7dae1bdd8ae7c6f Tue Oct 31 08:46:40 2023 -0700
    making FAQlink page for china, refs #32535
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 15, context: html, text, full: html, text
    e26cbe4b6258f09747ca7b01bc997c7c6a7472ad Tue Oct 31 14:00:22 2023 -0700
    Adding the filterType setting and making more updates to the decorator.html, refs #30237
  • lines changed 37, context: html, text, full: html, text
    7da083dc0686addd485ebf7367d18bc514be056b Tue Oct 31 15:51:58 2023 -0700
    Code review edits, updated quotes and removed <code> inside of <pre> lines, refs #32528
  • lines changed 18, context: html, text, full: html, text
    b811a0db8a37cdd07b4130f20e4568f253bdd6f3 Wed Nov 1 13:17:20 2023 -0700
    Adding <p> tags to keep the indentations consistent, refs #30237
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 14, context: html, text, full: html, text
    caec93e67f0067fd2363cf1faf4fa323b30d3716 Thu Nov 2 04:40:18 2023 -0700
    adapting more pages to china, refs #32535
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 43, context: html, text, full: html, text
    caec93e67f0067fd2363cf1faf4fa323b30d3716 Thu Nov 2 04:40:18 2023 -0700
    adapting more pages to china, refs #32535
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 26, context: html, text, full: html, text
    caec93e67f0067fd2363cf1faf4fa323b30d3716 Thu Nov 2 04:40:18 2023 -0700
    adapting more pages to china, refs #32535
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    d54773cbcf86ec999390a43f835f26a147131da6 Fri Oct 27 16:20:28 2023 -0700
    Updating GenArk paper link which was a preprint. Refs #32518
• src/hg/htdocs/images/feature_decorators.png
  • lines changed 0, context: html, text, full: html, text
    10fcec2865ff89952b6f94a4238fc65fcb8e1fc5 Tue Oct 31 11:33:35 2023 -0700
    Adding image for track decorators announcement, refs #32467
• src/hg/htdocs/images/videoIcon.png
  • lines changed 0, context: html, text, full: html, text
    ca43169b515fb278cade6884423e3f1c9bd83d58 Tue Oct 31 09:03:17 2023 -0700
    adding icon for local videos, refs #32535
• src/hg/htdocs/indexTraining.html
  • lines changed 13, context: html, text, full: html, text
    caec93e67f0067fd2363cf1faf4fa323b30d3716 Thu Nov 2 04:40:18 2023 -0700
    adapting more pages to china, refs #32535
• src/hg/htdocs/redmineWidget.html
  • lines changed 2, context: html, text, full: html, text
    f4c4cf6b48b0ae8f4e7424908ba8515af579a405 Fri Nov 3 13:22:40 2023 -0700
    Removing the widget from genome-preview as that is the machine the ITS scans and spams up, no RM.
  • lines changed 1, context: html, text, full: html, text
    11b3dab7c394f0cf5be4cfbdbf8d1d83b3ed2e0f Sat Nov 4 09:23:10 2023 -0700
    Fixing the src for the widget which was an accidental commit from some testing of mine with the new apache rules, no RM.
  • lines changed 1, context: html, text, full: html, text
    1f77f6826cae88613b6c24f8ac70cacf871230fa Sat Nov 4 11:04:49 2023 -0700
    Fixing the conditional statement for the widget to dissapear from genome-preview in preparation of the ITS security scan, email with Max and CA.
  • lines changed 1, context: html, text, full: html, text
    239e6c9466375cd289b51872833c07735c4f964a Sat Nov 4 13:24:34 2023 -0700
    Adding missing parenthesis for the rule to function properly, refs Max.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 6, context: html, text, full: html, text
    30a173751193022fc49b8162be99b9265b4d0901 Tue Oct 31 12:24:27 2023 -0700
    missed a CSS change in my last check-in
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    401691176ea0ade97d1c643bc2ed4c382fee1ef2 Fri Nov 3 16:59:50 2023 -0700
    Fix multi-term searches when using genomePosCJ: 1. make sure to collapse hgps together and combine highlight strings and item highlight names, 2. make sure hgSearch checks the json data returned during its init function if there was an error from the search term, such as different chromosomes for a multi-term search, refs #22978
• src/hg/js/hgc.js
  • lines changed 134, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
  • lines changed 1, context: html, text, full: html, text
    dad13f95ddaaa0f9c9b111fdc6454b0a3053c1c0 Tue Oct 31 10:56:18 2023 -0700
    Fix broken tables on hgc pages for tracks with the detailsDynamicTable setting, refs #32269,#32519
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    c92b5b790779371b350dbee33d0d7383d3bd6f91 Thu Nov 2 10:58:21 2023 -0700
    Fix mouseover pop up positioning when the pop up would normally be off the top of the window, refs #32011
  • lines changed 56, context: html, text, full: html, text
    7d7ba731c432325f1b3c235402a5af54b23e1ec7 Fri Nov 3 14:59:07 2023 -0700
    Make user clicks into an input or select or contextmenu make tooltips go away. Also decrease fudgeFactor on mousemove so tooltips are a little more senstitive and turn off faster, refs Max email
• src/hg/lib/chainArrange.as
  • lines changed 2, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
• src/hg/lib/chainArrange.c
  • lines changed 184, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/lib/chainArrange.h
  • lines changed 74, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/lib/chainArrange.sql
  • lines changed 22, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/lib/hdb.c
  • lines changed 10, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
  • lines changed 1, context: html, text, full: html, text
    b8058e48cdf423ddd5bbc3c9318251c523b7fbe4 Tue Oct 31 04:01:21 2023 -0700
    defaulting to TRUE for forceTwoBit, refs #22554
  • lines changed 3, context: html, text, full: html, text
    1eae44289e73a7f19aa794d5037d1c4f47d5ae31 Tue Oct 31 04:06:20 2023 -0700
    changes after code review, refs #32498, thanks to Braney
  • lines changed 1, context: html, text, full: html, text
    c7f117d5fc2aee9e65222776a7dae1bdd8ae7c6f Tue Oct 31 08:46:40 2023 -0700
    making FAQlink page for china, refs #32535
• src/hg/lib/hgHgvs.c
  • lines changed 50, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
  • lines changed 1, context: html, text, full: html, text
    d6dd43ca0436bf894bafe00cc5ee1398e3ead0d0 Tue Oct 31 09:51:12 2023 -0700
    Removing a redundant hAllocConn that caused a 'Too many open sqlConnections for cache' test failure.
  • lines changed 2, context: html, text, full: html, text
    c3c923b6c7177c78d5dd26d21f0c623a528ae6fe Tue Oct 31 14:49:09 2023 -0700
    Fix one bug found by Angie for historical transcript querying, should be checking for empty result, not NotEmpty result. Also sort quick query when user does not include a transcript version to order the results by newest historical transcripts first
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 33, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 29, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
  • lines changed 3, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
  • lines changed 8, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
  • lines changed 3, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 114, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/makeDb/trackDb/human/hg38/cancerExpr.ra
  • lines changed 2, context: html, text, full: html, text
    6f77a323aa436c278b61a8a4fad044b606507c45 Fri Nov 3 18:28:19 2023 -0700
    Fixing trackDb stanza which worked before, but correct formatting is to delcare the parent in the child track, not to have a superTrack setting on any children. No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 32, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
  • lines changed 2, context: html, text, full: html, text
    b8e4242557b46708572e17672d117b8a7de068a3 Thu Nov 2 15:25:22 2023 -0700
    Add link to gnomad for v4 vcf tracks, refs #32545
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 278, context: html, text, full: html, text
    a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 Wed Nov 1 16:30:45 2023 -0700
    Staging gnomad v4 vcfs track, refs #32545
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 117, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    1c85a7adb2c0f6681ad9b56fa1b6be264210200c Fri Nov 3 18:23:02 2023 -0700
    Fixing an issue in the way the trackDb was made. Apparently that way worked, but the children should not have the superTrack setting. They should only be declaring the parent. No RM.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 20, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/chainArrangeCollect/chainArrangeCollect.c
  • lines changed 111, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/utils/chainArrangeCollect/makefile
  • lines changed 3, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.err
  • lines changed 2, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 1, context: html, text, full: html, text
    62ccb95d5c71a3bf7658327e6db2bc35c19d1d71 Wed Oct 11 09:57:36 2023 -0700
    Adding back hgvs search support for historical refseq transcripts and historical refSeq transcripts track. Should be more resilient code this time.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
  • lines changed 2, context: html, text, full: html, text
    9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700
    Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
  • lines changed 6, context: html, text, full: html, text
    af90beb812e8f96e2283e62bd5082948ce455c58 Tue Oct 31 09:54:12 2023 -0700
    Updating default column offsets to match more recent nextclade versions
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 3, context: html, text, full: html, text
    9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700
    Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 3, context: html, text, full: html, text
    9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700
    Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 2, context: html, text, full: html, text
    9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700
    Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 11, context: html, text, full: html, text
    9a5ca254d03468faa1557b052349380a7067608e Tue Oct 31 09:57:03 2023 -0700
    Spare more sequences from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 11, context: html, text, full: html, text
    9fb2b35720b02cca3a9cece5cc8cdb782f86ed34 Tue Oct 31 09:56:35 2023 -0700
    Compress some previously uncompressed files so we don't waste quite so much disk space. Also spare sequences listed in sars-cov-2-variants/lineage-proposals repo file recombinants.tsv from the nextclade-based filters.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 43, context: html, text, full: html, text
    b7f10ba7db888f0fbaf5e49c7e42d7ad5291b1ac Tue Oct 31 09:52:22 2023 -0700
    More new lineages and a couple tweaks to old lineage paths.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
  • lines changed 1, context: html, text, full: html, text
    aa0dc230ac3da4b9ba3ab771afb381397da71c05 Tue Oct 31 09:57:35 2023 -0700
    Use compressed CNCB fasta.
• src/utils/bedCollect/bedCollect.c
  • lines changed 3, context: html, text, full: html, text
    b3af5822d95c94932b6d7b7abd93d1078bf251ee Mon Oct 30 16:55:40 2023 -0700
    changes in response to max review #32416
  • lines changed 110, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/utils/bedCollect/makefile
  • lines changed 3, context: html, text, full: html, text
    68684c7c01875a771889d1fd03354f58bae34427 Tue Oct 31 15:01:59 2023 -0700
    rename bedCollect to chainArrangeCollect in response to code review
• src/utils/qa/filterCartDumps.sh
  • lines changed 5, context: html, text, full: html, text
    57be65310f672a7a3f3ff9ee2169e3bcbe043004 Mon Oct 30 23:11:16 2023 -0700
    Adding the -L setting for curl and updating the output to display session URLs in the email, refs #31585
• src/utils/qa/hubPublicMail
  • lines changed 6, context: html, text, full: html, text
    215c24040415417ffb95e6b823a54b248147a5e8 Fri Oct 27 01:42:11 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix trying bugfix for hubPublicMail script for QA, email from Lou and Gera
  • lines changed 1, context: html, text, full: html, text
    216d3af107859db8cb1dd7e0376f2042c1b905a0 Mon Nov 6 09:25:39 2023 -0800
    Commenting out logging line so that we do not get emails every time the cron will email a hub provider. The reason is that we also see the email, so we are getting double notifications. No RM.
• src/utils/qa/longSessionCartDumps.sh
  • lines changed 1, context: html, text, full: html, text
    6865b9fc315a880361dcf52ed79fcfa2e2315d40 Mon Oct 30 23:01:19 2023 -0700
    Updating URL to have https. refs #31585
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a25bf51be0435edf6f8fcb71029698b8e1e36bd2 Mon Nov 6 09:59:41 2023 -0800
    v457 preview1

• lines changed: 1816
• files changed: 72