All File Changes

v466_base to v467_preview (2024-06-03 to 2024-06-10) v467

• src/hg/hgPhyloPlace/runUsher.c
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    e1ea58d34faf4e8fcbaa7a20d0a665575dfca76d Thu Jun 6 13:53:30 2024 -0700
    Fix: don't prepend server directory twice when telling server to reload protobufs.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    5cd6be21ca88d8aeb3ac9e179acd23d0af2272ed Thu Jun 6 16:28:17 2024 -0700
    Changing the name of the search button to Search to make it in line with our effort to sentence case the site, and also bring it in line with the new home page. No RM.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/htdocs/images/phylo/dm6_124way.png
  • lines changed 0, context: html, text, full: html, text
    f8fac38992ce22df69086505e80169743d57f3db Wed Jun 5 14:55:46 2024 -0700
    fix apiMel4 sciName from Anopheles_mellifera to Apis_mellifera refs #33933
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/htdocs/redmineWidget.html
  • lines changed 1, context: html, text, full: html, text
    621d571584c54c2114a233fcd74f83d11e5648b7 Thu Jun 6 10:00:00 2024 -0700
    Fixing the apache conditional statement, when I added hgwalpha I broke it so the security scan spammed us again. No RM.
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    311c682d1119b11a60f0585d129c0a01f5ebf600 Mon Jun 10 10:00:26 2024 -0700
    Check for undefined object member before calling string replace on it, refs #33216
• src/hg/js/utils.js
  • lines changed 30, context: html, text, full: html, text
    5ef3bb90e839f6d218c6ce5988adb111d600d3df Mon Apr 22 16:34:02 2024 -0700
    Make some special tooltips have a longer delay than normal item tooltips. This includes the track title tooltips.
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 87, context: html, text, full: html, text
    7e0b08b36c5ad87458c4f8845c6dc4a67864e4ed Mon Jun 10 10:05:56 2024 -0700
    Adding latest liftOver run between genark and native DBS refs #33945
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 6, context: html, text, full: html, text
    946b6507d4026812ec3f066120fb348d3d147c2e Wed Jun 5 10:25:58 2024 -0700
    adding six for a VGP update refs #29545
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 2, context: html, text, full: html, text
    d6207443ca5fe7eb379b9d8adc8ea8f53caccba8 Thu Jun 6 09:06:11 2024 -0700
    repeat modeler listings no longer available for VGP assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    946b6507d4026812ec3f066120fb348d3d147c2e Wed Jun 5 10:25:58 2024 -0700
    adding six for a VGP update refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 46, context: html, text, full: html, text
    da68b96458dabd2cee6f855ae603cd183fc37792 Tue Jun 4 12:36:15 2024 -0700
    Woops forgot makedoc when staging the gnomad v4.1 constraint tracks
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    946b6507d4026812ec3f066120fb348d3d147c2e Wed Jun 5 10:25:58 2024 -0700
    adding six for a VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    946b6507d4026812ec3f066120fb348d3d147c2e Wed Jun 5 10:25:58 2024 -0700
    adding six for a VGP update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    946b6507d4026812ec3f066120fb348d3d147c2e Wed Jun 5 10:25:58 2024 -0700
    adding six for a VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 71, context: html, text, full: html, text
    b39cc376c8eb72d6751b3c22dff4dd89b24e9367 Wed Jun 5 16:19:08 2024 -0700
    adding 57 for an update refs #29545
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    aa437ebc36c64962e2b4b8566f6960cf3a4b4915 Wed Jun 5 22:18:34 2024 -0700
    clean up legacy listings refs #29545
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    e220327e1a9df16032838380dffac1e44db86ecc Fri Jun 7 10:36:13 2024 -0700
    sorting out legacy assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 21, context: html, text, full: html, text
    aa437ebc36c64962e2b4b8566f6960cf3a4b4915 Wed Jun 5 22:18:34 2024 -0700
    clean up legacy listings refs #29545
  • lines changed 2, context: html, text, full: html, text
    e220327e1a9df16032838380dffac1e44db86ecc Fri Jun 7 10:36:13 2024 -0700
    sorting out legacy assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 177, context: html, text, full: html, text
    b39cc376c8eb72d6751b3c22dff4dd89b24e9367 Wed Jun 5 16:19:08 2024 -0700
    adding 57 for an update refs #29545
  • lines changed 13, context: html, text, full: html, text
    aa437ebc36c64962e2b4b8566f6960cf3a4b4915 Wed Jun 5 22:18:34 2024 -0700
    clean up legacy listings refs #29545
  • lines changed 7, context: html, text, full: html, text
    e220327e1a9df16032838380dffac1e44db86ecc Fri Jun 7 10:36:13 2024 -0700
    sorting out legacy assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 57, context: html, text, full: html, text
    b39cc376c8eb72d6751b3c22dff4dd89b24e9367 Wed Jun 5 16:19:08 2024 -0700
    adding 57 for an update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    aa437ebc36c64962e2b4b8566f6960cf3a4b4915 Wed Jun 5 22:18:34 2024 -0700
    clean up legacy listings refs #29545
• src/hg/makeDb/trackDb/human/covid.html
  • lines changed 5, context: html, text, full: html, text
    8cf469a79d1071bd5aab4072ae0ded8ef3f418e8 Thu Jun 6 17:48:00 2024 -0700
    Staging the work to nest all covid tracks into a single superTrack, refs #32887
• src/hg/makeDb/trackDb/human/covidHgiGwas.alpha.ra
  • lines changed 92, context: html, text, full: html, text
    8cf469a79d1071bd5aab4072ae0ded8ef3f418e8 Thu Jun 6 17:48:00 2024 -0700
    Staging the work to nest all covid tracks into a single superTrack, refs #32887
• src/hg/makeDb/trackDb/human/covidTracks.alpha.ra
  • lines changed 19, context: html, text, full: html, text
    8cf469a79d1071bd5aab4072ae0ded8ef3f418e8 Thu Jun 6 17:48:00 2024 -0700
    Staging the work to nest all covid tracks into a single superTrack, refs #32887
• src/hg/makeDb/trackDb/human/covidTracks.ra
  • lines changed 14, context: html, text, full: html, text
    8cf469a79d1071bd5aab4072ae0ded8ef3f418e8 Thu Jun 6 17:48:00 2024 -0700
    Staging the work to nest all covid tracks into a single superTrack, refs #32887
• src/hg/makeDb/trackDb/human/genCC.ra
  • lines changed 1, context: html, text, full: html, text
    06faf561c3dc3c6bfcd53428a73e637739d731e2 Tue Jun 4 01:23:09 2024 -0700
    Adding the acronyms to the longLabels based on feedback from user at ESHG2024. No RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    611da3ee2545caaf1a49f3d929d36e86016ad672 Tue Jun 4 01:18:45 2024 -0700
    adding LOEUF to gnomad tracks, LOEUF is the new and strongly recommended score and we have it, but forgot to chagne the long label, no redmine
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    a05d5d40647f7b2f1ec8e5667ecf3af8f5e03c84 Tue Jun 4 09:54:07 2024 -0700
    Change gnomad v4.1 variants bigBed mouseover after external feedback, refs Max email
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
  • lines changed 43, context: html, text, full: html, text
    23b210e9502fd4c00b524adf6940cea566ae1a95 Mon Jun 3 13:32:10 2024 -0700
    Stage v4.1 missense and pli by transcript tracks, #33823
  • lines changed 5, context: html, text, full: html, text
    611da3ee2545caaf1a49f3d929d36e86016ad672 Tue Jun 4 01:18:45 2024 -0700
    adding LOEUF to gnomad tracks, LOEUF is the new and strongly recommended score and we have it, but forgot to chagne the long label, no redmine
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    841a183a598b6b4e4339745df135d6900a244931 Fri Jun 7 09:45:34 2024 -0700
    Making the genomic codons appear by default, refs #33942
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 312, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
  • lines changed 3, context: html, text, full: html, text
    06faf561c3dc3c6bfcd53428a73e637739d731e2 Tue Jun 4 01:23:09 2024 -0700
    Adding the acronyms to the longLabels based on feedback from user at ESHG2024. No RM.
  • lines changed 16, context: html, text, full: html, text
    8cf469a79d1071bd5aab4072ae0ded8ef3f418e8 Thu Jun 6 17:48:00 2024 -0700
    Staging the work to nest all covid tracks into a single superTrack, refs #32887
• src/hg/makeDb/trackDb/jaspar.html
  • lines changed 312, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/makeDb/trackDb/jaspar.ra
  • lines changed 69, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/makeDb/trackDb/mouse/jaspar.html
  • lines changed 312, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM34.ra
  • lines changed 1, context: html, text, full: html, text
    c3bb4e5212585dc21a7e4f23db0978287ced674b Fri Jun 7 17:41:14 2024 -0700
    Releasing the latest GENCODE versions track, refs #33082
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e00c4ac98aed323e5dba0241250e4ee16369b573 Mon Jun 3 13:58:55 2024 -0700
    Combining all JASPAR tracks to use the same trackDb statement so we can setup automatic updates, refs #32537
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 4, context: html, text, full: html, text
    39232e1eb0b5b78c0e3f6ea360a5f70195f70840 Thu Jun 6 10:53:05 2024 -0700
    BA.2.86 representative has a name now. I removed 21627 (S:22) from BA.2.86's masking at @FedeGueli's request (sequences with mutation there were removed and added back).
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 49, context: html, text, full: html, text
    c7b3d23e420c71e53411d283b13ab3ac1c7ce84c Tue Jun 4 14:55:02 2024 -0700
    New lineages and a tweak to JN.1.39.1.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 3, context: html, text, full: html, text
    0b3aed10ba50cdda1d27a4b3cb170fbde09b6060 Thu Jun 6 10:55:24 2024 -0700
    Minor: move compression of new*.fa files into updateCombinedTree.sh to make manual copy-paste run completion a little easier.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 3, context: html, text, full: html, text
    0b3aed10ba50cdda1d27a4b3cb170fbde09b6060 Thu Jun 6 10:55:24 2024 -0700
    Minor: move compression of new*.fa files into updateCombinedTree.sh to make manual copy-paste run completion a little easier.
• src/hg/utils/overlapSelect/overlapSelect.c
  • lines changed 6, context: html, text, full: html, text
    fff0062e7c441f814c4aecfc74ac8ed60ae4eeb3 Wed Jun 5 03:41:37 2024 -0700
    add option for overlapSelect statistics output to have a TSV header on output
• src/hg/utils/overlapSelect/tests/expected/bed_over_NM_015110bedStatsTsvOutput.stats
  • lines changed 7, context: html, text, full: html, text
    fff0062e7c441f814c4aecfc74ac8ed60ae4eeb3 Wed Jun 5 03:41:37 2024 -0700
    add option for overlapSelect statistics output to have a TSV header on output
• src/hg/utils/overlapSelect/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    fff0062e7c441f814c4aecfc74ac8ed60ae4eeb3 Wed Jun 5 03:41:37 2024 -0700
    add option for overlapSelect statistics output to have a TSV header on output
• src/hg/utils/overlapSelect/usage.txt
  • lines changed 1, context: html, text, full: html, text
    fff0062e7c441f814c4aecfc74ac8ed60ae4eeb3 Wed Jun 5 03:41:37 2024 -0700
    add option for overlapSelect statistics output to have a TSV header on output
• src/utils/qa/jasparUpdate.py
  • lines changed 215, context: html, text, full: html, text
    b5d6d7abaeb13f8b9cf29db22c0827a54e66dcbc Fri Jun 7 14:33:09 2024 -0700
    Creating a script to automate the wrangling of the JASPAR transcription factor track. refs #32537
• src/utils/qa/makefile
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    6b776a1f0bcf1c245b4ee149981ac8549453b2ff Fri Jun 7 14:36:13 2024 -0700
    Adding the jasparUpdate.py script to the makefile, refs #32537
• src/utils/qa/weeklybld/buildEnv.csh
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    d7c1f69bc8e77131a9faf218ad96b1b6d9eadfd8 Mon Jun 10 10:18:11 2024 -0700
    v467 preview1, refs #33762

• lines changed: 2117
• files changed: 62