All File Changes

v461_base to v462_preview (2024-02-19 to 2024-02-26) v462

• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 18, context: html, text, full: html, text
    386b5d76ae4c1625e3da1421d4f2a73628ef6048 Wed Feb 21 14:06:22 2024 -0800
    Making cdwSubmit tag names against a schema file in the cdwSettings rather than hard-coded (and currently ifdefed out) tables.
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 1, context: html, text, full: html, text
    386b5d76ae4c1625e3da1421d4f2a73628ef6048 Wed Feb 21 14:06:22 2024 -0800
    Making cdwSubmit tag names against a schema file in the cdwSettings rather than hard-coded (and currently ifdefed out) tables.
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 99, context: html, text, full: html, text
    386b5d76ae4c1625e3da1421d4f2a73628ef6048 Wed Feb 21 14:06:22 2024 -0800
    Making cdwSubmit tag names against a schema file in the cdwSettings rather than hard-coded (and currently ifdefed out) tables.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    620a5662ff280f5ef66a061748b68e88c2824dfb Mon Feb 19 12:07:33 2024 -0800
    make sure coverage graphs always include zero
  • lines changed 1, context: html, text, full: html, text
    b9dd8c410acfb9a20dfb507b567a484b70a3c39b Tue Feb 20 12:36:29 2024 -0800
    check for NULL in exon mouseover code
  • lines changed 64, context: html, text, full: html, text
    7bed3b764ff1081822f1a43845464107d71528e9 Mon Feb 26 09:25:48 2024 -0800
    Add codon position information to genePred mouseovers, refs #32815
• src/hg/htdocs/covid19.html
  • lines changed 12, context: html, text, full: html, text
    7f49caee897fc87b9a1cdb24d9d83983b02c46f9 Mon Feb 26 03:31:59 2024 -0800
    china docs changes
  • lines changed 13, context: html, text, full: html, text
    7ab5023085cc60f8cae00bcd378187dac3921301 Mon Feb 26 03:32:59 2024 -0800
    china merge fix
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    552039db8b66654edeeea4a675815093d7c1c368 Tue Feb 20 08:23:07 2024 -0800
    Fixing stub for vcfPhasedTrio trackDb type definition, refs Max email
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    540c3402866777cffce61531fa9839a6aabc4357 Thu Feb 22 13:57:17 2024 -0800
    Acknowledging Ryan Collins for generating the data, refs #33044
• src/hg/inc/exportedDataHubs.h
  • lines changed 64, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    c49da1b974470a3aef749f0702ce2c23d3e8d7ea Sun Feb 25 11:19:48 2024 -0800
    Revert "get hgTrackUi to do the right thing if "type bigBed" is specified." This reverts commit f3c7b669da695e4919410f08f0a3f6fa21778796. Conflicts: src/hg/lib/trackDbCustom.c
  • lines changed 3, context: html, text, full: html, text
    9c21039dcd0fee54fdfd30253bc0088597df90e3 Sun Feb 25 11:48:47 2024 -0800
    another attempt to finish #19984
• src/hg/inc/quickLiftChain.h
  • lines changed 66, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/js/hgc.js
  • lines changed 2, context: html, text, full: html, text
    2480da67cb1c86aa07059664ea1ea07e43686090 Fri Feb 23 12:18:59 2024 -0800
    hgc's neato chain visualization matrix wasn't using the right track names
• src/hg/js/utils.js
  • lines changed 8, context: html, text, full: html, text
    89e3867fdfe87e87227745aeaa56f8fd9c43faec Tue Feb 20 14:28:30 2024 -0800
    Remove unused arguments and nop lines after mouseover refactoring, noticed by Angie's code review, refs #33002
• src/hg/lib/exportedDataHubs.as
  • lines changed 6, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/exportedDataHubs.c
  • lines changed 123, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/exportedDataHubs.sql
  • lines changed 12, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    c49da1b974470a3aef749f0702ce2c23d3e8d7ea Sun Feb 25 11:19:48 2024 -0800
    Revert "get hgTrackUi to do the right thing if "type bigBed" is specified." This reverts commit f3c7b669da695e4919410f08f0a3f6fa21778796. Conflicts: src/hg/lib/trackDbCustom.c
  • lines changed 21, context: html, text, full: html, text
    9c21039dcd0fee54fdfd30253bc0088597df90e3 Sun Feb 25 11:48:47 2024 -0800
    another attempt to finish #19984
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/quickLiftChain.as
  • lines changed 8, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/quickLiftChain.c
  • lines changed 139, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/quickLiftChain.sql
  • lines changed 16, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/lib/trackDbCustom.c
  • lines changed 9, context: html, text, full: html, text
    c49da1b974470a3aef749f0702ce2c23d3e8d7ea Sun Feb 25 11:19:48 2024 -0800
    Revert "get hgTrackUi to do the right thing if "type bigBed" is specified." This reverts commit f3c7b669da695e4919410f08f0a3f6fa21778796. Conflicts: src/hg/lib/trackDbCustom.c
  • lines changed 7, context: html, text, full: html, text
    9c21039dcd0fee54fdfd30253bc0088597df90e3 Sun Feb 25 11:48:47 2024 -0800
    another attempt to finish #19984
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 7, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    a1f4bdfbe157e1ffa563cb1c17277a8e0f64608a Wed Feb 21 07:55:55 2024 -0800
    continue VGP catch up adding a fish refs #29545
  • lines changed 1, context: html, text, full: html, text
    1581f886886465a884855e23d36e7ba86b1053e7 Thu Feb 22 11:42:58 2024 -0800
    VGP update adding a refseq replacement for GCA_028389875.1_bPtePen1.pri lesser rhea (bPtePen1 primary hap 2023) refs #29545
  • lines changed 21, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
  • lines changed 1, context: html, text, full: html, text
    1581f886886465a884855e23d36e7ba86b1053e7 Thu Feb 22 11:42:58 2024 -0800
    VGP update adding a refseq replacement for GCA_028389875.1_bPtePen1.pri lesser rhea (bPtePen1 primary hap 2023) refs #29545
  • lines changed 10, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/enigma.txt
  • lines changed 9, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
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    a1f4bdfbe157e1ffa563cb1c17277a8e0f64608a Wed Feb 21 07:55:55 2024 -0800
    continue VGP catch up adding a fish refs #29545
• src/hg/makeDb/doc/hg38/hprcQuickLift.txt
  • lines changed 11, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/makeDb/doc/hg38/makeExportHubs.txt
  • lines changed 16, context: html, text, full: html, text
    7d86e0ffbe4295c91220ff671c3eeb2009d41408 Sun Feb 25 11:09:39 2024 -0800
    working on quickLift UI
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    8fff54bd94620692c33ca61a765e6c0b6b5f7e2e Mon Feb 19 14:36:52 2024 -0800
    GCA_036323735.1_GRCr8 is now legacy refs #29545
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    db16a92829de8572ec6851100d0c36cbff4b679c Wed Feb 21 13:19:08 2024 -0800
    lesser rhea bird became refseq refs #29545
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    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    db16a92829de8572ec6851100d0c36cbff4b679c Wed Feb 21 13:19:08 2024 -0800
    lesser rhea bird became refseq refs #29545
  • lines changed 1, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ceb56b8ba253193567799661e5bad75c3eb17a3b Tue Feb 20 12:00:26 2024 -0800
    VGP update refs #29545
  • lines changed 6, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt
  • lines changed 3, context: html, text, full: html, text
    8cf5d04b02f2bacf4fb496891d9cfc3cd99e8df8 Tue Feb 20 10:33:36 2024 -0800
    recover from otto update refs #32902
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    bed61f703ece9dceb41a80e602672b1a46cd4dba Tue Feb 20 13:42:26 2024 -0800
    recover a broken assembly refs #29545
  • lines changed 13, context: html, text, full: html, text
    6a5231ee061fec8de66664cb9194bd4a7f958beb Mon Feb 26 09:29:26 2024 -0800
    catch up VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 42, context: html, text, full: html, text
    b7834b8f15822ed19ccfd6fb1ac210dd80ac6938 Mon Feb 19 15:38:21 2024 -0800
    update adding about 40 assemblies no redmine
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    907878c0e305c60aa4c3aa34716bf4bcbf3ba1a3 Tue Feb 20 14:18:17 2024 -0800
    catching up 9 assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 4, context: html, text, full: html, text
    79742b17c9cf66a054d07369d0141836ce2752fb Mon Feb 19 15:08:20 2024 -0800
    catching up four assemblies no redmine
  • lines changed 42, context: html, text, full: html, text
    b7834b8f15822ed19ccfd6fb1ac210dd80ac6938 Mon Feb 19 15:38:21 2024 -0800
    update adding about 40 assemblies no redmine
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    907878c0e305c60aa4c3aa34716bf4bcbf3ba1a3 Tue Feb 20 14:18:17 2024 -0800
    catching up 9 assemblies refs #29545
• src/hg/makeDb/scripts/enigma/BRCAclinDomains.py
  • lines changed 66, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/scripts/enigma/BRCAexonWeights.py
  • lines changed 113, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/scripts/enigma/BRCAfunctionalAssays.py
  • lines changed 154, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/scripts/enigma/BRCAmla.py
  • lines changed 175, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/scripts/enigma/BRCAsplicing.py
  • lines changed 164, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/makeDb/trackDb/human/hg38/multiz100Logo.ra
  • lines changed 48, context: html, text, full: html, text
    a764282569227de6bddc449427b869e0ca512ab1 Tue Feb 20 12:20:29 2024 -0800
    remove multiz logo prototype tracks
• src/hg/makeDb/trackDb/human/hg38/multiz30Logo.ra
  • lines changed 48, context: html, text, full: html, text
    a764282569227de6bddc449427b869e0ca512ab1 Tue Feb 20 12:20:29 2024 -0800
    remove multiz logo prototype tracks
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 52, context: html, text, full: html, text
    a764282569227de6bddc449427b869e0ca512ab1 Tue Feb 20 12:20:29 2024 -0800
    remove multiz logo prototype tracks
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    a764282569227de6bddc449427b869e0ca512ab1 Tue Feb 20 12:20:29 2024 -0800
    remove multiz logo prototype tracks
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    9c7cf25466929f9fd3137c3c131943b6b8c1ff17 Fri Feb 23 12:24:42 2024 -0800
    take out experimental HPRC chains tracks
• src/hg/makeDb/trackDb/human/trackDb.enigmaTracks.ra
  • lines changed 60, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
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    bf5fc23cef14d9555d2ba4edbd7368a1e73334eb Thu Feb 22 15:25:54 2024 -0800
    Adding visibilities to the subtracks, refs #32919
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    57105e3e6e8c590537fedcc559cb0fac2812d56d Thu Feb 22 14:33:24 2024 -0800
    Staging the ENIGMA tracks, refs #32919
• src/hg/utils/exportedTracks/exportedTracks.as
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    c2f9a4ebe3f08ac661f2927860d73289072532c7 Fri Feb 23 12:20:12 2024 -0800
    first cut
• src/hg/utils/makefile
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    00d972032daa3a173a3142bb4f7923f259caf312 Wed Feb 21 11:56:22 2024 -0800
    add bigChainToChain to userApps build no redmine
• src/hg/utils/otto/omim/doOmimGene2.sh
  • lines changed 2, context: html, text, full: html, text
    568230c7e381feb1e4dc69b598579cb20083b05c Fri Feb 23 11:32:55 2024 -0800
    Fixing an otto job, no RM.
• src/hg/utils/otto/uniprot/doUniprot
  • lines changed 21, context: html, text, full: html, text
    ef33c128a8aee1ba566ffa9f8e088888c07001c4 Mon Feb 26 03:31:08 2024 -0800
    fixing bug in uniprot otto job. the md5 of fasta files was not working, as some fastas entries look like ">uniprotId isRef" and other sequences dont have this "isRef" word. This meant that for the reference sequences, the sequence was not used for the md5 but only the word isRef. This meant that the otto job missed a change in a genome if only a single reference sequence changed. this will lead to a recompute of absolutely every mapping file at the next otto run and will use up the cluster for a few days. Oops.
• src/product/installer/browserSetup.sh
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    64877d44db2ed81b8451f9431d342a93a8b67188 Mon Feb 19 09:26:19 2024 -0800
    adding support for RHEL to GBIC, no redmine
• src/utils/hubMake/hubMake
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    2717829315a39adf14be0ad4745acf5a9d17583e Tue Feb 20 10:48:12 2024 -0800
    updates to hubMake
• src/utils/qa/weeklybld/buildEnv.csh
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    fd53c173b1ec8d8cec51a0ae69cfca584121c91f Mon Feb 26 11:10:13 2024 -0800
    v462 preview1, refs #32981

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• files changed: 75