All File Changes

v412_preview2 to v412_base (2021-03-15 to 2021-03-22) v412

• confs/hgwdev.hg.conf
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    c94bc55b94145ae633c2bd105d7d85415325cefd Sun Mar 21 01:11:48 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/blat/version.doc
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    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/expected/testDynServer.out
  • lines changed 1, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/expected/testDynServerPcr.out
  • lines changed 1, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/expected/testDynServerPerSeqMax.out
  • lines changed 1, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/expected/testDynServerTrans.out
  • lines changed 1, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/expected/testDynServerWithDir.out
  • lines changed 1, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/testDynServer
  • lines changed 2, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/testDynServerPcr
  • lines changed 2, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/testDynServerPerSeqMax
  • lines changed 2, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/testDynServerTrans
  • lines changed 2, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/gfServer/tests/testDynServerWithDir
  • lines changed 2, context: html, text, full: html, text
    9a1029b1c89bb9c8aa387cd20c2e83f8c21c546a Mon Mar 15 16:36:03 2021 -0700
    make gfServer tests insensitive to version changes
• src/hg/hgBlat/hgBlat.c
  • lines changed 12, context: html, text, full: html, text
    6b9b7637b977bdc62cb2d447e3a6c2766cac414c Thu Mar 18 14:45:26 2021 -0700
    Make dynamic blat explanation very minimal. refs #26658
  • lines changed 5, context: html, text, full: html, text
    cf45361ec82056f4fac5342e94b16c6e437c58e9 Thu Mar 18 16:47:52 2021 -0700
    finishing touches on hgBlat Search All verbiage and FAQ links added. refs #26658
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    d6c0b0e804ffa16adefe2703385685945323ca39 Wed Mar 17 11:37:32 2021 -0700
    Added missing NULL check (for uploaded sequences that failed QC checks).
• src/hg/hgSession/hgSession.c
  • lines changed 0, context: html, text, full: html, text
    81a974138f95b555fbeab5907367cd3d5eeb89a6 Mon Mar 15 16:28:56 2021 -0700
    grammar tweak. backup is a noun and an adjective but not a verb
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    9adbcfa9d9ea587304395ebc95a641777f3b8b41 Mon Mar 15 20:41:15 2021 -0700
    Add Cancel button to multi-region config popup, by request of JK. refs #26385
  • lines changed 5, context: html, text, full: html, text
    ed39331147a0cd7868921ef7bdf6b3f022a49c1b Tue Mar 16 18:10:57 2021 -0700
    Customize multi-region config help message to current status and disable exit button when not in MR mode. refs #26385
  • lines changed 17, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/hgTracks/pubsTracks.c
  • lines changed 1, context: html, text, full: html, text
    edaa869d45d9c67e23efb5b2704e3b91d4ef4cdb Tue Mar 16 09:29:49 2021 -0700
    pubs track was trying to free memory that was never allocated now that we use the trackDb cache, refs Lou email
  • lines changed 1, context: html, text, full: html, text
    4d8aafef6108905a734e61f6781600234e72719f Wed Mar 17 12:08:48 2021 -0700
    Fixing compile warning about unused variable that broke the build.
  • lines changed 1, context: html, text, full: html, text
    ba27f0347009225d2875121c56cfc93d96a9f7de Wed Mar 17 12:19:57 2021 -0700
    Removing unneeded declaration that I should have removed in edaa869d4, refs Kate email
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 1, context: html, text, full: html, text
    d388bde7f71e98a337eb5c89ddaf7be200d8493c Thu Mar 18 12:22:13 2021 -0700
    Fixing extra definition of xlab in boxplot() function for barChart tracks, refs #27230
  • lines changed 1, context: html, text, full: html, text
    9d88e0062744b8dea79861cb32836424485f2ebd Thu Mar 18 13:10:00 2021 -0700
    When overwriting barChart boxplot labels with empty value because we draw custom ones later, I forgot to override the y-label value for new vertical boxplots, refs #27149
  • lines changed 1, context: html, text, full: html, text
    33f33d948046c72f6689fc277b7ea31873b5cc1d Thu Mar 18 13:12:00 2021 -0700
    Fixing typo in previous commit, forgot a comma, refs #27149
  • lines changed 3, context: html, text, full: html, text
    db643eee1acb462313f15f2ab7570c66238c0205 Thu Mar 18 17:35:44 2021 -0700
    Ensure consistent treatment of underscores and spaces in boxplot, refs #27214
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 9, context: html, text, full: html, text
    cf45361ec82056f4fac5342e94b16c6e437c58e9 Thu Mar 18 16:47:52 2021 -0700
    finishing touches on hgBlat Search All verbiage and FAQ links added. refs #26658
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 5, context: html, text, full: html, text
    1be61b371f81c9281c681fbf008f4676d487c7fd Thu Feb 25 16:11:35 2021 -0800
    added some clarifying text
• src/hg/htdocs/goldenPath/help/covidBrowser.html
  • lines changed 268, context: html, text, full: html, text
    b7afc005b6fd12992034a9e915c1a93d3f75e978 Thu Mar 18 13:37:22 2021 -0700
    Creating a copy stub to be edited in the future at the request of Isabel, Alexis, and Clay. refs #27233
• src/hg/htdocs/goldenPath/help/covidBrowserIntro.html
  • lines changed 16, context: html, text, full: html, text
    d5b482e55f12f625e0c94de419a58d8a1d746791 Thu Mar 11 14:08:56 2021 -0800
    Adding links to hgTracks etx. refs #27173
  • lines changed 1, context: html, text, full: html, text
    50b498ed99557aa0cd1ee5476b51395b0ad07418 Wed Mar 17 16:13:31 2021 -0700
    Adding news annoucement, link fix for covid, and last minute changes for knownGene refs #26919
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 0, context: html, text, full: html, text
    81a974138f95b555fbeab5907367cd3d5eeb89a6 Mon Mar 15 16:28:56 2021 -0700
    grammar tweak. backup is a noun and an adjective but not a verb
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 2, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 2, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    837957371f3d3becdd9c17ed746d6a311950da48 Mon Mar 15 16:30:54 2021 -0700
    Making changes as per code review refs #27204
  • lines changed 3, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    47506be1baa258c868a8d845bfd5bcc6b4465f58 Wed Mar 17 10:37:55 2021 -0700
    Editing the 072420 refSeq diffs announcement, refs #22586
  • lines changed 26, context: html, text, full: html, text
    50b498ed99557aa0cd1ee5476b51395b0ad07418 Wed Mar 17 16:13:31 2021 -0700
    Adding news annoucement, link fix for covid, and last minute changes for knownGene refs #26919
  • lines changed 11, context: html, text, full: html, text
    dee1b87619f6cb852ae6574a1abed1a019072042 Thu Mar 18 14:56:43 2021 -0700
    Updated to kg announcement refs #26919
  • lines changed 44, context: html, text, full: html, text
    7bd1e1a311d07a946fb7b4be7eeadbd500335c2e Thu Mar 18 15:16:55 2021 -0700
    Announcing the miRNA track for hg19, refs #26287
  • lines changed 1, context: html, text, full: html, text
    550260758374599a0caeeb496a2b1e810f0b908b Thu Mar 18 16:15:48 2021 -0700
    Adding date to Jairo's newsarch No RM
  • lines changed 36, context: html, text, full: html, text
    163a294300cc27dbcc4b9501aac95630bb765d5f Fri Mar 19 16:57:03 2021 -0700
    Announcng GENCODE update refs #27008 #27007 #27006
• src/hg/htdocs/images/staff2021.jpg
  • lines changed 0, context: html, text, full: html, text
    04c4f17ef56844363297aa4ac7444f5e7e799e0c Mon Mar 15 13:32:47 2021 -0700
    Adding staff2021.jpg image refs #27091
• src/hg/htdocs/indexNews.html
  • lines changed 8, context: html, text, full: html, text
    50b498ed99557aa0cd1ee5476b51395b0ad07418 Wed Mar 17 16:13:31 2021 -0700
    Adding news annoucement, link fix for covid, and last minute changes for knownGene refs #26919
  • lines changed 19, context: html, text, full: html, text
    7bd1e1a311d07a946fb7b4be7eeadbd500335c2e Thu Mar 18 15:16:55 2021 -0700
    Announcing the miRNA track for hg19, refs #26287
  • lines changed 11, context: html, text, full: html, text
    163a294300cc27dbcc4b9501aac95630bb765d5f Fri Mar 19 16:57:03 2021 -0700
    Announcng GENCODE update refs #27008 #27007 #27006
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    2f08eaa28a96367f826b4328fd69e6fd7a1b9430 Mon Mar 15 16:15:25 2021 -0700
    Adding Manager to Lou's title at Bob's request CR refs #27204
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    ed39331147a0cd7868921ef7bdf6b3f022a49c1b Tue Mar 16 18:10:57 2021 -0700
    Customize multi-region config help message to current status and disable exit button when not in MR mode. refs #26385
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    3c35fb1a00fbb4ecf3701e2679b62a3c5aacab40 Mon Mar 22 13:26:35 2021 -0700
    New version number v412
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    9adbcfa9d9ea587304395ebc95a641777f3b8b41 Mon Mar 15 20:41:15 2021 -0700
    Add Cancel button to multi-region config popup, by request of JK. refs #26385
  • lines changed 30, context: html, text, full: html, text
    ed39331147a0cd7868921ef7bdf6b3f022a49c1b Tue Mar 16 18:10:57 2021 -0700
    Customize multi-region config help message to current status and disable exit button when not in MR mode. refs #26385
• src/hg/js/utils.js
  • lines changed 12, context: html, text, full: html, text
    d53f7ac6b0845499960d6ce6d9c8e04324145706 Mon Mar 22 13:17:48 2021 -0700
    Don't warn the same message multiple times in the hgTracks warn box, refs #27247
• src/hg/lib/googleAnalytics.c
  • lines changed 4, context: html, text, full: html, text
    0e6a03b8f0c8f6a307a01b8780195680e32bcb76 Mon Mar 22 04:23:41 2021 -0700
    adding outlink tracking to hgTrackUi, refs #21916
• src/hg/lib/haploinsufficiency.as
  • lines changed 15, context: html, text, full: html, text
    a80b1e18948fdd1bccec83660a5ca3db9628f95a Thu Mar 18 23:10:50 2021 -0700
    Supporting files and makedoc update for DECIPHER haploinsufficiency, refs #25707
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    a2cbff13a70c454dfb455027e96bd5afe7a01170 Tue Mar 16 16:42:27 2021 -0700
    Fix up relatedTracks section on hgTrackUi/hgc pages to not choke on superTracks, and don't show duplicate tracks, refs #25721
  • lines changed 4, context: html, text, full: html, text
    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/makeDb/doc/calJac4/genes.txt
  • lines changed 12, context: html, text, full: html, text
    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/doc/hg19.txt
  • lines changed 35, context: html, text, full: html, text
    a7533ba73cff353b993553668f9fb21df243f71b Thu Mar 18 09:54:14 2021 -0700
    Makedoc for DECIPHER haploinsufficiency on hg19, refs #25707
  • lines changed 4, context: html, text, full: html, text
    a80b1e18948fdd1bccec83660a5ca3db9628f95a Thu Mar 18 23:10:50 2021 -0700
    Supporting files and makedoc update for DECIPHER haploinsufficiency, refs #25707
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 2, context: html, text, full: html, text
    7c11083c038619e6d2d3fa03f216b98570be0668 Sun Mar 14 14:23:24 2021 -0700
    clean up a couple of things from VM26 import
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    7c11083c038619e6d2d3fa03f216b98570be0668 Sun Mar 14 14:23:24 2021 -0700
    clean up a couple of things from VM26 import
• src/hg/makeDb/trackDb/human/hg19/decipherHaploIns.html
  • lines changed 49, context: html, text, full: html, text
    a80b1e18948fdd1bccec83660a5ca3db9628f95a Thu Mar 18 23:10:50 2021 -0700
    Supporting files and makedoc update for DECIPHER haploinsufficiency, refs #25707
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 2, context: html, text, full: html, text
    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    a344378d46082c009cc0e7fa992d24412809c741 Thu Mar 18 15:18:24 2021 -0700
    Releasing the miRNA track for hg19, refs #26287
  • lines changed 10, context: html, text, full: html, text
    a80b1e18948fdd1bccec83660a5ca3db9628f95a Thu Mar 18 23:10:50 2021 -0700
    Supporting files and makedoc update for DECIPHER haploinsufficiency, refs #25707
  • lines changed 11, context: html, text, full: html, text
    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV37lift37.ra
  • lines changed 1, context: html, text, full: html, text
    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 1, context: html, text, full: html, text
    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra
  • lines changed 1, context: html, text, full: html, text
    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    15bf75f348f58b87e55619c5a051f2080851f1fe Fri Mar 19 15:44:37 2021 -0700
    Continued organizing hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
  • lines changed 142, context: html, text, full: html, text
    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 48, context: html, text, full: html, text
    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 168, context: html, text, full: html, text
    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
  • lines changed 142, context: html, text, full: html, text
    ec8051253e871b92e4b3ca0394d33fda3ee4f4e0 Tue Mar 16 15:53:17 2021 -0700
    Reverting knownGene versioning refs #26919
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 49, context: html, text, full: html, text
    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
  • lines changed 50, context: html, text, full: html, text
    ec8051253e871b92e4b3ca0394d33fda3ee4f4e0 Tue Mar 16 15:53:17 2021 -0700
    Reverting knownGene versioning refs #26919
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    50b498ed99557aa0cd1ee5476b51395b0ad07418 Wed Mar 17 16:13:31 2021 -0700
    Adding news annoucement, link fix for covid, and last minute changes for knownGene refs #26919
• src/hg/makeDb/trackDb/human/hg38/knownGeneV32.html
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    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
• src/hg/makeDb/trackDb/human/hg38/knownGeneV32.ra
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    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
• src/hg/makeDb/trackDb/human/hg38/knownGeneV36.html
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    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
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    ec8051253e871b92e4b3ca0394d33fda3ee4f4e0 Tue Mar 16 15:53:17 2021 -0700
    Reverting knownGene versioning refs #26919
• src/hg/makeDb/trackDb/human/hg38/knownGeneV36.ra
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    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
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    ec8051253e871b92e4b3ca0394d33fda3ee4f4e0 Tue Mar 16 15:53:17 2021 -0700
    Reverting knownGene versioning refs #26919
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    b007d778ad754a8bf78ef98e8aac64b47c4d912b Tue Mar 16 15:38:52 2021 -0700
    Pushing knownGene trackDb modifications for Gencode v36 with new versioned names #26919
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    ec8051253e871b92e4b3ca0394d33fda3ee4f4e0 Tue Mar 16 15:53:17 2021 -0700
    Reverting knownGene versioning refs #26919
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV37.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
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    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/human/trackDb.ra
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    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
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    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/marmoset/calJac4/catV2.html
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    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.isoseq.ra
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    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
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    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.uwIsoSeq.ra
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    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/trackDb/marmoset/calJac4/uwIsoSeq.html
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    ebf4d53739b5e2cae52a51d50236c80c29c88e0f Fri Mar 19 16:07:25 2021 -0700
    added calJac4 CAT genes and Iso-Seq alignments
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    3212aa13fdd28e55f0641ed0d134ce3efc14fa35 Fri Mar 19 09:49:46 2021 -0700
    Organized mm10 non-default tracks in alphabetical order, refs #19187
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    44e6f33c2a2ab5900fac360bcf2623518d51939a Fri Mar 19 12:36:24 2021 -0700
    Continued organizing mm10 non-default tracks in alphabetical order, refs #19187
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    1a31f2d78739ee1706430f1203da97fe6fb36d15 Fri Mar 19 15:57:28 2021 -0700
    One more track to change to alphabetical order, refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
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    3212aa13fdd28e55f0641ed0d134ce3efc14fa35 Fri Mar 19 09:49:46 2021 -0700
    Organized mm10 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
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    3212aa13fdd28e55f0641ed0d134ce3efc14fa35 Fri Mar 19 09:49:46 2021 -0700
    Organized mm10 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    3212aa13fdd28e55f0641ed0d134ce3efc14fa35 Fri Mar 19 09:49:46 2021 -0700
    Organized mm10 non-default tracks in alphabetical order, refs #19187
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    44e6f33c2a2ab5900fac360bcf2623518d51939a Fri Mar 19 12:36:24 2021 -0700
    Continued organizing mm10 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM26.ra
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    105989fddf202b197c20e681d391fcb1ecfd9d67 Fri Mar 19 12:44:24 2021 -0700
    Viz changes in prep for GENCODE release for hg38/hg19/mm39. Refs #27006
• src/hg/makeDb/trackDb/relatedTracks.ra
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    955a3cec3464b317fd2ed0f84470f59b820aed1e Thu Mar 18 15:19:17 2021 -0700
    Removing the duplicate TS sites and gene example, refs #25721
• src/hg/makeDb/trackDb/tagTypes.tab
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    8ae222adb54c0234afbe72e49a50da755c272352 Wed Mar 17 17:30:41 2021 -0700
    1. Add checkbox to multi-region config custom regions panel that causes display to show all regions. This is under same hg.conf control as multi-region button move 2. Change multiRegionBedUrl track setting to match existing cart var (multiRegionsBedUrl). Tweak help text on MR config panel, as per QA input. refs #26385
• src/hg/makeDb/trackDb/trackDb.genbank.ra
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    d63e61cdc4fa118eee44f5074a7f5bf0aeb0f5df Fri Mar 19 00:38:12 2021 -0700
    Organized the hg19 and hg38 non-default tracks in alphabetical order, refs #19187
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    097d4692aba233d7e2cc9e39cbcd11eefe2d76ca Tue Mar 16 11:20:03 2021 -0700
    Adding pennantIcon for swift primer track refs #27178
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    64ef1345bfa1476ad1c2a1ad7cf413e95556966b Wed Mar 17 11:53:07 2021 -0700
    We can actually end up with more bioSamples than we're looking for due to including past results, so compare IDs instead of counts.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    30ebf52c1ccbd592b814c18d3a68c30624a0f85d Wed Mar 17 11:55:37 2021 -0700
    Adding new updateCombinedTree.sh after updatePublicTree.sh for GISAID+public tree. Eventually, public tree will be derived from combined tree.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    e9b05abd1cee4cdf715a0dd725332f507b2141a3 Wed Mar 17 11:52:03 2021 -0700
    Don't need -x anymore, too verbose.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    30ebf52c1ccbd592b814c18d3a68c30624a0f85d Wed Mar 17 11:55:37 2021 -0700
    Adding new updateCombinedTree.sh after updatePublicTree.sh for GISAID+public tree. Eventually, public tree will be derived from combined tree.
• src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
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    02d1894196c846ac4eedfee782ff1bf182f2adbf Wed Mar 17 11:56:18 2021 -0700
    Tolerate another condition where grep finding 0 results crashed the script.
• src/hg/utils/otto/sarscov2phylo/util.sh
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    c218231e30bb4cbc6e6536738585b3df1b3f673c Wed Mar 17 11:51:18 2021 -0700
    Make cleanGenbank ~10x more efficient by splitting out sed commands to take advantage of many cores, and adding a test and branch to the slowest command.
• src/inc/cheapcgi.h
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    9adbcfa9d9ea587304395ebc95a641777f3b8b41 Mon Mar 15 20:41:15 2021 -0700
    Add Cancel button to multi-region config popup, by request of JK. refs #26385
• src/inc/srcVersion.h
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    3c35fb1a00fbb4ecf3701e2679b62a3c5aacab40 Mon Mar 22 13:26:35 2021 -0700
    New version number v412
• src/lib/cheapcgi.c
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    9adbcfa9d9ea587304395ebc95a641777f3b8b41 Mon Mar 15 20:41:15 2021 -0700
    Add Cancel button to multi-region config popup, by request of JK. refs #26385
• src/utils/qa/linkCheckExclude
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    3fcc103e9979d4739fed3a5810855696fb3f62d6 Tue Mar 16 11:53:41 2021 -0700
    Updating excluded list for htmlCheck cronjob
• src/utils/qa/weeklybld/buildEnv.csh
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    011d5eab1d2806bcd6e82c19a0fa64ed86bc6323 Mon Mar 22 13:25:33 2021 -0700
    v412 final build, refs #27172
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    00005b72fb81425da34d48f77c518af8e6c3928d Fri Mar 19 13:59:05 2021 -0700
    add defaultCart to standard hgcentral tables

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