All File Changes

v460_preview2 to v460_base (2024-01-22 to 2024-01-29) v460

• python/style.txt
  • lines changed 105, context: html, text, full: html, text
    9cd22e907ddc25e36dcd18c493631aa457acbd6d Mon Jan 29 08:14:25 2024 -0800
    updating python style guide
• src/hg/hgBlat/hgBlat.c
  • lines changed 14, context: html, text, full: html, text
    9893abd21ce01ced9a71dbefb55f8a76ab2e0e60 Mon Jan 29 05:58:17 2024 -0800
    adding links to isPcr, shortMatch and findMotifs on hgBlat error message, refs #32918
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    2f0e8762dff89ffadfbfabdff2cdde7ee09f073c Fri Jan 26 02:53:04 2024 -0800
    adding assembly to hgTrackUi page, refs #32893
• src/hg/hgTracks/bamTrack.c
  • lines changed 9, context: html, text, full: html, text
    8f86c2b590033a0f28d6c47dfece59b51528193b Fri Jan 26 10:51:00 2024 -0800
    some tweaks to coverage mode.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    5d067524b02b43961a9ba64f677dd0334760c056 Thu Jan 25 11:54:06 2024 -0800
    Updating error message, refs #32854
  • lines changed 16, context: html, text, full: html, text
    a33f1b928200549e10005e79e6db16a9d79b801e Thu Jan 25 13:37:37 2024 -0800
    use summary information in bigBeds when filters are off and there are too many items in the region
  • lines changed 1, context: html, text, full: html, text
    8f86c2b590033a0f28d6c47dfece59b51528193b Fri Jan 26 10:51:00 2024 -0800
    some tweaks to coverage mode.
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    b5ef1b8aaf9bfc4c37bc290e9a9da1aeb89b56b1 Thu Jan 25 04:19:40 2024 -0800
    hide back to genome browser link as per QA, refs #32926
• src/hg/hgTracks/simpleTracks.c
  • lines changed 52, context: html, text, full: html, text
    d540e9dca3211faf36fab80fa3b640d4bd6ee288 Tue Jan 23 06:18:20 2024 -0800
    adding phase mouseover, refs #32487
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    c3d8cab7fb381aa72fdccaa4078333d5968be24c Wed Jan 24 09:12:05 2024 -0800
    limit maxItems to 10,000
  • lines changed 1, context: html, text, full: html, text
    c49e15f509c78230ed67bfc87093a36de1f0dcf6 Wed Jan 24 13:50:09 2024 -0800
    make vcTabix use coverage mode correctly
  • lines changed 1, context: html, text, full: html, text
    2a1bdd799264439afd96294f275fae89a77bb1e3 Thu Jan 25 04:28:34 2024 -0800
    string changes as per anna, refs #32487
  • lines changed 29, context: html, text, full: html, text
    a33f1b928200549e10005e79e6db16a9d79b801e Thu Jan 25 13:37:37 2024 -0800
    use summary information in bigBeds when filters are off and there are too many items in the region
• src/hg/hgTracks/variation.c
  • lines changed 10, context: html, text, full: html, text
    8f86c2b590033a0f28d6c47dfece59b51528193b Fri Jan 26 10:51:00 2024 -0800
    some tweaks to coverage mode.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    987c2646ca9a9b97c5b37d80a4f71f52ac157427 Tue Jan 23 06:06:02 2024 -0800
    changes after code review, refs #32873
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    91151694a4cd74a60ce01b2c1e13756eb2c86802 Mon Jan 22 15:12:46 2024 -0800
    Adding final feedback for the release of new HPRC tracks, refs #32287
  • lines changed 3, context: html, text, full: html, text
    b80137060da6eaa02e20272671b45db104f26691 Mon Jan 22 15:36:56 2024 -0800
    Fixing some small typos, no RM
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    414d03c4d766381c49b1de6aaf9fbaf550b47998 Tue Jan 23 02:14:41 2024 -0800
    oligoMatch tweak in menu, refs #32893
  • lines changed 1, context: html, text, full: html, text
    2635cd08d23b245b3720223f06e8a84db8f08d4a Tue Jan 23 02:16:23 2024 -0800
    uppercasing, refs #32893
  • lines changed 1, context: html, text, full: html, text
    b5ef1b8aaf9bfc4c37bc290e9a9da1aeb89b56b1 Thu Jan 25 04:19:40 2024 -0800
    hide back to genome browser link as per QA, refs #32926
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    9ec2d3b4769060d4397f24cce21b14cf520e7a63 Mon Jan 29 11:16:10 2024 -0800
    New version number v460
• src/hg/js/hgTracks.js
  • lines changed 16, context: html, text, full: html, text
    063fd84b2d90c8991a78b23b11e92c52cbac0ac3 Tue Jan 23 06:16:16 2024 -0800
    renaming right-click options, refs #32487
  • lines changed 2, context: html, text, full: html, text
    e52566237fd2912438ea38bd14ff6e7619b61597 Thu Jan 25 13:46:43 2024 -0800
    Renaming right-click exon/codon options, refs #32487
  • lines changed 4, context: html, text, full: html, text
    b5ca727e4c614bc40ee46ef96bdac3972ca21225 Fri Jan 26 10:26:18 2024 -0800
    More edits to the names for the right-click exon/codon options, refs #32487
• src/hg/js/utils.js
  • lines changed 7, context: html, text, full: html, text
    a90b29ffd9e8db10f6e15aca0f74497772ad8c3c Mon Jan 22 16:06:30 2024 -0800
    Delete old debug code that was unused and fix typo from not properly deleting the debuggin code, refs #32697
  • lines changed 1, context: html, text, full: html, text
    a8c513765a4a49ef7cd0395922f96453acce922c Mon Jan 22 16:12:18 2024 -0800
    Woops, was too hasty in removing code in the last commit, refs #32697
  • lines changed 1, context: html, text, full: html, text
    2e609c69e2e33c01daa54b21ee4e2a71ddf6d639 Tue Jan 23 10:24:53 2024 -0800
    Don't add an empty hubUrl to track search hgTracks form unless there really was a hub result that was clicked on, refs #32909
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    d778a2e4f1057843a549fff1b92037d609a6fc10 Tue Jan 23 07:31:01 2024 -0800
    the default is now to NOT trust trackDb
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    c49e15f509c78230ed67bfc87093a36de1f0dcf6 Wed Jan 24 13:50:09 2024 -0800
    make vcTabix use coverage mode correctly
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 9, context: html, text, full: html, text
    c5434ed7a6bace4f29fcd2de7efc8babb82cf070 Tue Jan 23 10:31:37 2024 -0800
    nine new assemblies from the T2T primates project refs #29545
  • lines changed 1, context: html, text, full: html, text
    3dbd31c2d1698c2ed69cfac5e8ff12c0b791210d Tue Jan 23 18:16:11 2024 -0800
    adding T2T primate GCA_028858825.2_NHGRI_mPanPan1-v2.0_pat refs #29545
  • lines changed 4, context: html, text, full: html, text
    c44ff63a8459b35e4ca895eb9d32c3a12b5d7b2e Wed Jan 24 13:18:27 2024 -0800
    final T2T primate assembly GCA_028858845.2_NHGRI_mPanPan1-v2.0_mat refs #29545
  • lines changed 5, context: html, text, full: html, text
    8dd8b5446255e693537853a18599daf1041ecbf3 Sat Jan 27 08:28:55 2024 -0800
    adding four Oxytricha trigallax and the gigantic European mistletoe refs #29545
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 18, context: html, text, full: html, text
    e68b8a55273a3b04eb0560a2a40115540ce1dca0 Tue Jan 23 14:28:04 2024 -0800
    Making the Affy CytoScan HD track for hg38, refs #32856
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    8dd8b5446255e693537853a18599daf1041ecbf3 Sat Jan 27 08:28:55 2024 -0800
    adding four Oxytricha trigallax and the gigantic European mistletoe refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 7, context: html, text, full: html, text
    c5434ed7a6bace4f29fcd2de7efc8babb82cf070 Tue Jan 23 10:31:37 2024 -0800
    nine new assemblies from the T2T primates project refs #29545
  • lines changed 1, context: html, text, full: html, text
    e0304789c866a4bf80f48372c733f78b2b0ce544 Wed Jan 24 10:08:28 2024 -0800
    three new gorilla assemblies from T2T primates project refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    c5434ed7a6bace4f29fcd2de7efc8babb82cf070 Tue Jan 23 10:31:37 2024 -0800
    nine new assemblies from the T2T primates project refs #29545
  • lines changed 1, context: html, text, full: html, text
    e0304789c866a4bf80f48372c733f78b2b0ce544 Wed Jan 24 10:08:28 2024 -0800
    three new gorilla assemblies from T2T primates project refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8dd8b5446255e693537853a18599daf1041ecbf3 Sat Jan 27 08:28:55 2024 -0800
    adding four Oxytricha trigallax and the gigantic European mistletoe refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    c5434ed7a6bace4f29fcd2de7efc8babb82cf070 Tue Jan 23 10:31:37 2024 -0800
    nine new assemblies from the T2T primates project refs #29545
  • lines changed 1, context: html, text, full: html, text
    3dbd31c2d1698c2ed69cfac5e8ff12c0b791210d Tue Jan 23 18:16:11 2024 -0800
    adding T2T primate GCA_028858825.2_NHGRI_mPanPan1-v2.0_pat refs #29545
  • lines changed 3, context: html, text, full: html, text
    e0304789c866a4bf80f48372c733f78b2b0ce544 Wed Jan 24 10:08:28 2024 -0800
    three new gorilla assemblies from T2T primates project refs #29545
  • lines changed 1, context: html, text, full: html, text
    c44ff63a8459b35e4ca895eb9d32c3a12b5d7b2e Wed Jan 24 13:18:27 2024 -0800
    final T2T primate assembly GCA_028858845.2_NHGRI_mPanPan1-v2.0_mat refs #29545
• src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
  • lines changed 18, context: html, text, full: html, text
    e68b8a55273a3b04eb0560a2a40115540ce1dca0 Tue Jan 23 14:28:04 2024 -0800
    Making the Affy CytoScan HD track for hg38, refs #32856
  • lines changed 3, context: html, text, full: html, text
    65a83976bd296811b06171e0911a3c5574d81a1a Tue Jan 23 14:49:52 2024 -0800
    Updating the hg38 Affy CytoScan HD track description, refs #32856
• src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    47d29f27937fd038ebecc65d5e8afec1c053e59c Tue Jan 23 02:32:11 2024 -0800
    tdb rename hprc, refs #32287
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    e68b8a55273a3b04eb0560a2a40115540ce1dca0 Tue Jan 23 14:28:04 2024 -0800
    Making the Affy CytoScan HD track for hg38, refs #32856
• src/hg/utils/automation/asmHubRmodelJoinAlign.pl
  • lines changed 1, context: html, text, full: html, text
    cfe4c0816778b8d58fe613cb8f4d221ca8a4f312 Thu Jan 25 15:28:45 2024 -0800
    spell check refs #32871
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 3, context: html, text, full: html, text
    335d4c88dcce7148ccb0f6df4a18a2881b2075f7 Wed Jan 24 11:34:06 2024 -0800
    Check number of columns when reading auxillary tab files. This caused use of uninitialized memory, inserting garbage and ocassional newlines in BED file
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 31, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
  • lines changed 1, context: html, text, full: html, text
    d8a01805f188894f0a2dbdbafefe3b522874fa28 Thu Jan 25 13:57:24 2024 -0800
    removed use of RefSeq standard_name in generating names, there are some cases were it contains long english phrase
• src/hg/utils/gff3ToGenePred/tests/expected/discontinuousTest.gp
  • lines changed 3, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/frameShiftTest.gp
  • lines changed 8, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/geneTranscriptTest.gp
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.attrs
  • lines changed 101, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.gp
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/minimalGenesTest.gp
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/multCdsOutOfExonTest.out
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs
  • lines changed 158, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
  • lines changed 84, context: html, text, full: html, text
    d8a01805f188894f0a2dbdbafefe3b522874fa28 Thu Jan 25 13:57:24 2024 -0800
    removed use of RefSeq standard_name in generating names, there are some cases were it contains long english phrase
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp
  • lines changed 13, context: html, text, full: html, text
    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
  • lines changed 7, context: html, text, full: html, text
    d8a01805f188894f0a2dbdbafefe3b522874fa28 Thu Jan 25 13:57:24 2024 -0800
    removed use of RefSeq standard_name in generating names, there are some cases were it contains long english phrase
• src/hg/utils/gff3ToGenePred/tests/expected/noExonsTest.gp
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/gff3ToGenePred/tests/input/noId.gff3
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    b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800
    try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
• src/hg/utils/otto/clinvar/clinVarToBed
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    a916136b8536d1cea475bd82516fa751726b414b Wed Jan 24 08:33:49 2024 -0800
    adding stars to clinvar, refs #32915
• src/inc/srcVersion.h
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    9ec2d3b4769060d4397f24cce21b14cf520e7a63 Mon Jan 29 11:16:10 2024 -0800
    New version number v460
• src/product/installer/browserSetup.sh
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    28c1e8bc50ff54c6672c27d6aa8c56f8c2ae2bf9 Wed Jan 24 09:06:49 2024 -0800
    gbic fix: if curl already exists, allow yum to replace it, no redmine
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    452e0a315bf47b4c995fc793db3066ae6e2db082 Wed Jan 24 09:08:43 2024 -0800
    gbic fix: some minimal linuxes have no initscripts yet, no redmine
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    343643df48f155c6003939fa808aebfea651b239 Wed Jan 24 09:26:03 2024 -0800
    gbic fix: suppress interactive prompt on new jimmy ubuntu
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    55d2d8fea0ceb0069d98e241e8a5234638478a53 Wed Jan 24 09:34:15 2024 -0800
    gbic fix: prefer service over systemd commands, as docker containers do not have systemd at all, no redmine
• src/utils/qa/makefile
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    d122f99d0953b764550091651e882f03af2453fb Wed Jan 24 14:05:59 2024 -0800
    Adding new script that parses track counts to report either 1. The amount of usage over a period of time, or 2. Report a number of tracks under a certain threshold. This is to be used in determining tracks that we should hide, nest, depracate or archive. Refs #32813
• src/utils/qa/qaTestScript.py
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    6612fc9f15c280c9744b236db1a86f07bd8a27b5 Thu Jan 25 09:24:01 2024 -0800
    Adding search queries that caused hgTracks crash, refs ##32891
• src/utils/qa/trackCountsParse
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    d122f99d0953b764550091651e882f03af2453fb Wed Jan 24 14:05:59 2024 -0800
    Adding new script that parses track counts to report either 1. The amount of usage over a period of time, or 2. Report a number of tracks under a certain threshold. This is to be used in determining tracks that we should hide, nest, depracate or archive. Refs #32813
• src/utils/qa/weeklybld/buildEnv.csh
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    49939ea923fc665216218a371fa2ef69710b1b97 Mon Jan 29 11:15:19 2024 -0800
    v460 final build, refs #32867

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• files changed: 75