All File Changes

v462_preview to v462_preview2 (2024-02-26 to 2024-03-04) v462

• confs/asia.hg.conf
  • lines changed 7, context: html, text, full: html, text
    4f4b346461ccd03fb2874ac91e78dd13335689c6 Sun Mar 3 01:11:26 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 7, context: html, text, full: html, text
    4f4b346461ccd03fb2874ac91e78dd13335689c6 Sun Mar 3 01:11:26 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 10, context: html, text, full: html, text
    4f4b346461ccd03fb2874ac91e78dd13335689c6 Sun Mar 3 01:11:26 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 9, context: html, text, full: html, text
    4f4b346461ccd03fb2874ac91e78dd13335689c6 Sun Mar 3 01:11:26 2024 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 9, context: html, text, full: html, text
    4f4b346461ccd03fb2874ac91e78dd13335689c6 Sun Mar 3 01:11:26 2024 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    7338fb10bb7ffdc0a75445a36cd128e6be593d36 Mon Feb 26 10:51:47 2024 -0800
    fix a bunch of places that were printing out hub_#_db instead of just db
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    7338fb10bb7ffdc0a75445a36cd128e6be593d36 Mon Feb 26 10:51:47 2024 -0800
    fix a bunch of places that were printing out hub_#_db instead of just db
• src/hg/hgTables/schema.c
  • lines changed 3, context: html, text, full: html, text
    7338fb10bb7ffdc0a75445a36cd128e6be593d36 Mon Feb 26 10:51:47 2024 -0800
    fix a bunch of places that were printing out hub_#_db instead of just db
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    36174525f6181ecb2412a076afdf755dc226fdcd Wed Feb 28 14:48:09 2024 -0800
    Do not try to figure out bigBed type number for super tracks, refs #19984
  • lines changed 4, context: html, text, full: html, text
    ee948d8cdfadb0cfb6dcf44147d8e6dfeca3b5cc Wed Feb 28 15:08:16 2024 -0800
    take out bigBed field recogntion for the moment as it is making the browser sllllooooww
• src/hg/hgTracks/cds.c
  • lines changed 3, context: html, text, full: html, text
    61f9643c131fb8ff8d1fbf75d8562c98668d61c7 Mon Feb 26 13:14:46 2024 -0800
    Make codon numbers in mouseovers show up at the cds color level and not just the cds number level, fix incorrect mouseovers on introns that was broken by previous change, refs #32815
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    db848693861a76988a11bd1bf26cbd45a4451215 Fri Mar 1 06:25:59 2024 -0800
    outputting link to hub desc in bluebar group, refs #33065
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    cd8ab617cef63bd0c925c1f67e9fafe5c086d583 Mon Feb 26 11:19:13 2024 -0800
    Fix condition for whether we should print codon numbers in mouseover, refs #32815
  • lines changed 2, context: html, text, full: html, text
    61f9643c131fb8ff8d1fbf75d8562c98668d61c7 Mon Feb 26 13:14:46 2024 -0800
    Make codon numbers in mouseovers show up at the cds color level and not just the cds number level, fix incorrect mouseovers on introns that was broken by previous change, refs #32815
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    7338fb10bb7ffdc0a75445a36cd128e6be593d36 Mon Feb 26 10:51:47 2024 -0800
    fix a bunch of places that were printing out hub_#_db instead of just db
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 13, context: html, text, full: html, text
    b866b80e5a3d77797edd9c29ecf7eae04e6c6daf Fri Mar 1 19:23:36 2024 -0800
    added a bit of details to CRAM refUrl to make it a bit clearer
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    b866b80e5a3d77797edd9c29ecf7eae04e6c6daf Fri Mar 1 19:23:36 2024 -0800
    added a bit of details to CRAM refUrl to make it a bit clearer
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    db848693861a76988a11bd1bf26cbd45a4451215 Fri Mar 1 06:25:59 2024 -0800
    outputting link to hub desc in bluebar group, refs #33065
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    5534d8dbbffc4d47d416eb4d75e981d10c9a8145 Tue Feb 27 15:58:38 2024 -0800
    Fix labelByCfgUi to ignore composite tracks. This removes an unnecessary stack dump from the error logs, refs #30612
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    db848693861a76988a11bd1bf26cbd45a4451215 Fri Mar 1 06:25:59 2024 -0800
    outputting link to hub desc in bluebar group, refs #33065
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    7338fb10bb7ffdc0a75445a36cd128e6be593d36 Mon Feb 26 10:51:47 2024 -0800
    fix a bunch of places that were printing out hub_#_db instead of just db
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    ca772477b6c6c8aad194cf39f03a20d64822b535 Wed Feb 28 11:22:36 2024 -0800
    adding two per user request refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    b57ac0715b42f8f23e512e2c9bdb312b48d1933d Wed Feb 28 11:44:47 2024 -0800
    Staging gnomAD v2.1.1 non-cancer filter set, ready for QA, refs #32916
  • lines changed 24, context: html, text, full: html, text
    ceaab2e2802978958ae88c4ee012337c8342bbb0 Fri Mar 1 15:55:22 2024 -0800
    Adding makedoc for the BayesDel track and the Prediction Scores track, refs #27766
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 7, context: html, text, full: html, text
    0fa824c87481cee76efea38dc2dc5214b8f94457 Mon Mar 4 09:18:39 2024 -0800
    Add constraint scores makedoc, refs #33084
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    ca772477b6c6c8aad194cf39f03a20d64822b535 Wed Feb 28 11:22:36 2024 -0800
    adding two per user request refs #29545
• src/hg/makeDb/gnomad/combine.awk
  • lines changed 3, context: html, text, full: html, text
    73ecf418edee1ae991841f9bbf6ec5fe623407ec Fri Mar 1 15:24:02 2024 -0800
    Staging gnomAD v4 constraint track on test, refs #33084
• src/hg/makeDb/outside/bayesDel/hg19/createMaxAFBayesDelWig.py
  • lines changed 111, context: html, text, full: html, text
    81ecb5a305ecfc8e3dbd6af02b8d16f96c34926a Wed Feb 28 09:49:45 2024 -0800
    Adding python files for the BayesDel track in the kent tree, refs #27766
• src/hg/makeDb/outside/bayesDel/hg19/createNoAFBayesDelWig.py
  • lines changed 109, context: html, text, full: html, text
    81ecb5a305ecfc8e3dbd6af02b8d16f96c34926a Wed Feb 28 09:49:45 2024 -0800
    Adding python files for the BayesDel track in the kent tree, refs #27766
• src/hg/makeDb/trackDb/human/hg19/bayesDel.ra
  • lines changed 108, context: html, text, full: html, text
    8306ec3081bb1de2baa64ee1c45849f2b04cb3db Wed Feb 28 12:01:08 2024 -0800
    Making the BayesDel track for hg19, refs #32856
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 31, context: html, text, full: html, text
    b57ac0715b42f8f23e512e2c9bdb312b48d1933d Wed Feb 28 11:44:47 2024 -0800
    Staging gnomAD v2.1.1 non-cancer filter set, ready for QA, refs #32916
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 33, context: html, text, full: html, text
    73ecf418edee1ae991841f9bbf6ec5fe623407ec Fri Mar 1 15:24:02 2024 -0800
    Staging gnomAD v4 constraint track on test, refs #33084
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 1, context: html, text, full: html, text
    2bde85a34b8accbea0c60266f90af25d911cee12 Fri Mar 1 15:23:12 2024 -0800
    Small edit to human/jaspar.html and major edits to mouse/jaspar.html
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
  • lines changed 4, context: html, text, full: html, text
    f986caf1879bd73d9be8f9b54e8cb92ad20d1025 Mon Mar 4 09:55:46 2024 -0800
    Removing release tags for the JASPAR 2024 track, refs #31973
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 89, context: html, text, full: html, text
    8306ec3081bb1de2baa64ee1c45849f2b04cb3db Wed Feb 28 12:01:08 2024 -0800
    Making the BayesDel track for hg19, refs #32856
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 10, context: html, text, full: html, text
    8306ec3081bb1de2baa64ee1c45849f2b04cb3db Wed Feb 28 12:01:08 2024 -0800
    Making the BayesDel track for hg19, refs #32856
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    8306ec3081bb1de2baa64ee1c45849f2b04cb3db Wed Feb 28 12:01:08 2024 -0800
    Making the BayesDel track for hg19, refs #32856
• src/hg/makeDb/trackDb/mouse/jaspar.html
  • lines changed 94, context: html, text, full: html, text
    2bde85a34b8accbea0c60266f90af25d911cee12 Fri Mar 1 15:23:12 2024 -0800
    Small edit to human/jaspar.html and major edits to mouse/jaspar.html
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
  • lines changed 4, context: html, text, full: html, text
    f986caf1879bd73d9be8f9b54e8cb92ad20d1025 Mon Mar 4 09:55:46 2024 -0800
    Removing release tags for the JASPAR 2024 track, refs #31973
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 39, context: html, text, full: html, text
    6bf6c4a5a5fc30bdc36c46d97c054e71a4e430f2 Fri Mar 1 17:56:04 2024 -0800
    knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
  • lines changed 22, context: html, text, full: html, text
    96d42a83504a06ff88f7003117db9cc3ff0209c4 Fri Mar 1 17:59:55 2024 -0800
    Archive of previous mm39 knownGene, VM33, refs #32415
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    a6120bfa3829d90ae7f989c783e0584b746fe2e2 Wed Feb 28 23:37:42 2024 -0800
    Updating the transcription factor gene names in alphabetical order for JASPAR2024 track, refs #31973
  • lines changed 2, context: html, text, full: html, text
    6bf6c4a5a5fc30bdc36c46d97c054e71a4e430f2 Fri Mar 1 17:56:04 2024 -0800
    knownGene trackDb
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    2be287f9ae16a4fed9c8446dd702a1dbfc1335ab Tue Feb 27 16:14:23 2024 -0800
    Add .WAIT keyword between all's cgi and utils dependencies, in hopes that we won't have two parallel paths building hgLoadWiggle at the same time. refs #33064
• src/hg/pslCheck/pslCheck.c
  • lines changed 13, context: html, text, full: html, text
    24cf4a1294b7e146f488b877eb87b9f2e83eaa9c Wed Feb 28 17:39:28 2024 -0800
    moving static loadSizes() function from hg/utils/pslCheck.c to lib/common.c no redmine
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 7, context: html, text, full: html, text
    fe83e4d06fbda0328582179c72c789b1552cea52 Fri Feb 23 15:25:04 2024 -0800
    More requested masked sites/ranges/reversions for BA.2.86.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 22, context: html, text, full: html, text
    82ed492d276b1f4c52c88840f6006f72b4b3321b Fri Feb 23 15:25:44 2024 -0800
    More new recombinants to spare from the perhaps overly stringent reversions filter.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 9, context: html, text, full: html, text
    3d44b701513a615e6733228f78f104e99e091142 Wed Feb 14 19:27:26 2024 -0800
    Last batch of new lineages in pango-designation v1.25.
  • lines changed 8, context: html, text, full: html, text
    ada071f1d68622f6ca492dd6cb289fc71b9a6021 Fri Feb 23 15:24:10 2024 -0800
    Ongoing new lineages.
• src/hg/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c
  • lines changed 12, context: html, text, full: html, text
    164d54ed22c894be328c9c4d7ebcdbc9c40f407e Thu Feb 29 10:53:41 2024 -0800
    loadSizes is now a src/hg/common.c function refs #33064
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    24cf4a1294b7e146f488b877eb87b9f2e83eaa9c Wed Feb 28 17:39:28 2024 -0800
    moving static loadSizes() function from hg/utils/pslCheck.c to lib/common.c no redmine
• src/inc/common.mk
  • lines changed 43, context: html, text, full: html, text
    808b2080cee27e44ce67dd1c2efbf5dcdf7d3a09 Mon Feb 26 13:39:00 2024 -0800
    recovering the build on Darwin after OS upgrades no redmine
  • lines changed 25, context: html, text, full: html, text
    d68fdca16fd97881c20eaf95c2a431d6536e1fa4 Mon Feb 26 17:29:51 2024 -0800
    refining the build on Mac OSX no redmine
• src/lib/common.c
  • lines changed 14, context: html, text, full: html, text
    24cf4a1294b7e146f488b877eb87b9f2e83eaa9c Wed Feb 28 17:39:28 2024 -0800
    moving static loadSizes() function from hg/utils/pslCheck.c to lib/common.c no redmine
• src/utils/bamToPsl/bamToPsl.c
  • lines changed 22, context: html, text, full: html, text
    b766d400687cd499a41a895f249557e49a381d72 Wed Feb 28 18:13:55 2024 -0800
    allow bamToPsl to fixup qSize when given a querySizes file no redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    e47a87f34f7b6b4e7987e7a067c9e61d72d892a7 Mon Mar 4 10:15:40 2024 -0800
    v462 preview2, refs #33051

• lines changed: 990
• files changed: 61