All File Changes

v478_preview to v478_preview2 (2025-02-10 to 2025-02-17) v478

• src/hg/cgilib/cartEdit7.c
  • lines changed 38, context: html, text, full: html, text
    98e34d21f00b90814efdb0a1a032b0cd0525f59c Sat Feb 15 13:49:45 2025 -0800
    add cart rewrite for the introduction of spliceImpactSuper
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    98e34d21f00b90814efdb0a1a032b0cd0525f59c Sat Feb 15 13:49:45 2025 -0800
    add cart rewrite for the introduction of spliceImpactSuper
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    98e34d21f00b90814efdb0a1a032b0cd0525f59c Sat Feb 15 13:49:45 2025 -0800
    add cart rewrite for the introduction of spliceImpactSuper
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 8, context: html, text, full: html, text
    4a46f573e0253d75a6137b7fd0ec92eff1a97017 Tue Feb 11 14:08:27 2025 -0800
    Small touches to cdwMakeValidFile.c to pass through xls and raw format without validation for SSPsyGene
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 1, context: html, text, full: html, text
    6990d48baaf213bbcdcfc1c69f933abe1654fe12 Thu Feb 13 13:18:29 2025 -0800
    Adding to cdwSubmit.c otherSupportedFormats raw and xls to bypass error Format X is not supported
• src/hg/hgCollection/hgCollection.c
  • lines changed 9, context: html, text, full: html, text
    7204d8c80f457039e942c33cb832900010a65270 Thu Feb 13 12:33:50 2025 -0800
    don't create hub in hgCollection on invocation. Wait till something gets added to the collection. Refs #35088
• src/hg/hgConvert/hgConvert.c
  • lines changed 8, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgTables/bigBed.c
  • lines changed 5, context: html, text, full: html, text
    7ac9dba0abbb050561bb41ea08d98fa76a27d4cb Thu Feb 13 03:03:31 2025 -0800
    improvements to data schema page to make it easier for users to convert and download big data, refs #35223
• src/hg/hgTables/bigWig.c
  • lines changed 1, context: html, text, full: html, text
    7ac9dba0abbb050561bb41ea08d98fa76a27d4cb Thu Feb 13 03:03:31 2025 -0800
    improvements to data schema page to make it easier for users to convert and download big data, refs #35223
• src/hg/hgTables/hgTables.c
  • lines changed 3, context: html, text, full: html, text
    7ac9dba0abbb050561bb41ea08d98fa76a27d4cb Thu Feb 13 03:03:31 2025 -0800
    improvements to data schema page to make it easier for users to convert and download big data, refs #35223
• src/hg/hgTables/hgTables.h
  • lines changed 7, context: html, text, full: html, text
    7ac9dba0abbb050561bb41ea08d98fa76a27d4cb Thu Feb 13 03:03:31 2025 -0800
    improvements to data schema page to make it easier for users to convert and download big data, refs #35223
• src/hg/hgTables/schema.c
  • lines changed 9, context: html, text, full: html, text
    7ac9dba0abbb050561bb41ea08d98fa76a27d4cb Thu Feb 13 03:03:31 2025 -0800
    improvements to data schema page to make it easier for users to convert and download big data, refs #35223
• src/hg/hgTracks/bedTrack.c
  • lines changed 2, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 2, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgc/bigBedClick.c
  • lines changed 2, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 33, context: html, text, full: html, text
    ebf7c2678556d6eae1e6521f317977fd1c9cdc88 Sun Feb 16 09:56:46 2025 -0800
    adding entry about running blat locally, refs #34829
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 2, context: html, text, full: html, text
    88bee298da706e1f201cd33de416a9159ee83a92 Wed Feb 12 12:21:56 2025 -0800
    Updating the documentation of which Linux distributions are supported for GBiC, refs #35034
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 6, context: html, text, full: html, text
    88bee298da706e1f201cd33de416a9159ee83a92 Wed Feb 12 12:21:56 2025 -0800
    Updating the documentation of which Linux distributions are supported for GBiC, refs #35034
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    2569546173bc8da0f0421a6874d9d68532b9693b Wed Feb 12 05:03:38 2025 -0800
    fixing newsArch for gene dosage track, no redmine
  • lines changed 26, context: html, text, full: html, text
    6b78f9e2a0f72fb96422140882f9db9517473f4c Fri Feb 14 13:59:59 2025 -0800
    Announcing the CIViC track for hg38 and hg19, refs #34371
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    6b78f9e2a0f72fb96422140882f9db9517473f4c Fri Feb 14 13:59:59 2025 -0800
    Announcing the CIViC track for hg38 and hg19, refs #34371
• src/hg/inc/hubConnect.h
  • lines changed 2, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/inc/quickLift.h
  • lines changed 6, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/js/hgCollection.js
  • lines changed 1, context: html, text, full: html, text
    7204d8c80f457039e942c33cb832900010a65270 Thu Feb 13 12:33:50 2025 -0800
    don't create hub in hgCollection on invocation. Wait till something gets added to the collection. Refs #35088
• src/hg/js/hgMyData.js
  • lines changed 1, context: html, text, full: html, text
    4c2a1ad09c702610de592ce31b18d9efdd630404 Mon Feb 10 14:42:22 2025 -0800
    Fix bug in hubSpace UI so file sizes are pretty printed, refs #31058
  • lines changed 6, context: html, text, full: html, text
    046cb646c41a37610f2aba0d335238b59eabd655 Mon Feb 10 17:17:23 2025 -0800
    Stop uploads early if they would exceed the quota, refs #31058
  • lines changed 62, context: html, text, full: html, text
    157b3e782017ad059b88a62fa75a349874188d4d Fri Feb 14 12:23:00 2025 -0800
    Calculate hubSpace directory size in UI as size of all child files, refs #31058
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    7745870ea056cab7527a5421f625d5780877662e Thu Feb 13 12:36:24 2025 -0800
    protect function from getting called with a NULL
  • lines changed 7, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/lib/quickLift.c
  • lines changed 12, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/lib/trackHub.c
  • lines changed 10, context: html, text, full: html, text
    6823728f16334d9b53bd595688c8f5780cf833fe Sun Feb 16 12:13:13 2025 -0800
    ongoing work on quickLift. Added support for SQL beds
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 45, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
  • lines changed 9, context: html, text, full: html, text
    bc16781521899fc09b02eeb7e48084072e55b103 Thu Feb 13 11:52:07 2025 -0800
    updates for VGP and user request refs #29545
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 4, context: html, text, full: html, text
    7654d51ae443fa237818e2660877f9ccf777c6b5 Mon Feb 10 11:19:06 2025 -0800
    prevent user.hub.txt from going out refs #34917
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    bc16781521899fc09b02eeb7e48084072e55b103 Thu Feb 13 11:52:07 2025 -0800
    updates for VGP and user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
• src/hg/makeDb/doc/hg38/civic.txt
  • lines changed 1, context: html, text, full: html, text
    1a5e2c957cbe91c24163d3df7532e57b85f47c2d Tue Feb 11 02:34:59 2025 -0800
    adding note about civic being on otto
• src/hg/makeDb/doc/hg38/mitoMap.txt
  • lines changed 24, context: html, text, full: html, text
    2596c3765d9f8fb8ffe464d7d11ba843374f672a Wed Feb 12 12:49:11 2025 -0800
    MITOMAP track is now ready for QA, refs #24849
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 4, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 19, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    6c0d1a1c493b1194a548772fe51958103c9fb348 Tue Feb 11 15:03:49 2025 -0800
    working on a VGP update refs #29545
  • lines changed 9, context: html, text, full: html, text
    bc16781521899fc09b02eeb7e48084072e55b103 Thu Feb 13 11:52:07 2025 -0800
    updates for VGP and user request refs #29545
• src/hg/makeDb/hgGoldGapGl/makefile
  • lines changed 1, context: html, text, full: html, text
    a3dc6f427dd906f15647f68eda2fb4b75ece6ffd Mon Feb 10 15:22:59 2025 -0800
    fixed a broken makefile and so other improvements from code review
• src/hg/makeDb/hgLoadWiggle/makefile
  • lines changed 1, context: html, text, full: html, text
    a3dc6f427dd906f15647f68eda2fb4b75ece6ffd Mon Feb 10 15:22:59 2025 -0800
    fixed a broken makefile and so other improvements from code review
  • lines changed 5, context: html, text, full: html, text
    83dfd584fdce8632dd2eb11c7d1ddb66c227c13f Mon Feb 10 16:17:26 2025 -0800
    put back non-standard test target, but the test do not run, so commented it out
• src/hg/makeDb/scripts/buildMitoMap.py
  • lines changed 256, context: html, text, full: html, text
    2596c3765d9f8fb8ffe464d7d11ba843374f672a Wed Feb 12 12:49:11 2025 -0800
    MITOMAP track is now ready for QA, refs #24849
• src/hg/makeDb/trackDb/human/abSplice.alpha.ra
  • lines changed 17, context: html, text, full: html, text
    eed605180384e7782a79dde4a364e7c82a0c647d Mon Feb 10 22:20:22 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 17, context: html, text, full: html, text
    54f66cad4f181133ae0afc8a55695adfd649e3ba Mon Feb 10 22:28:46 2025 -0800
    Revert "Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823" This reverts commit eed605180384e7782a79dde4a364e7c82a0c647d.
  • lines changed 17, context: html, text, full: html, text
    08be5093ab6c4535c129810cc78f840c5aca3c8a Thu Feb 13 14:19:52 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
• src/hg/makeDb/trackDb/human/alphaMissense.html
  • lines changed 12, context: html, text, full: html, text
    be9c66b2a69ce9479e4830f5a0d36d9a26d67969 Sun Feb 16 10:50:26 2025 -0800
    very minor formatting changes for desc page, refs #32269
• src/hg/makeDb/trackDb/human/alphaMissense.ra
  • lines changed 0, context: html, text, full: html, text
    875ca5fc8aa85486a89e261f3fa843f86a962091 Sun Feb 16 10:05:29 2025 -0800
    changing some tabs to spaces, refs #32269
• src/hg/makeDb/trackDb/human/civic.html
  • lines changed 6, context: html, text, full: html, text
    cb4c5ca53034c40e1255903d5c993aff2c49d053 Mon Feb 10 16:09:38 2025 -0800
    Adding a link to the CIViC website to the track description page. Fixing a few typos in the text. Replacing double quotes with the HTML entity. refs #34371
  • lines changed 1, context: html, text, full: html, text
    011899189339ecebc9973c24bd650dc63e1bbe50 Thu Feb 13 14:24:37 2025 -0800
    Fixing a typo in the CIViC track, refs #34371
  • lines changed 21, context: html, text, full: html, text
    4fdeb1e794284d5c342a8c8863d895d6b44dbeb3 Thu Feb 13 14:40:54 2025 -0800
    Adding missing </p> tags. Changing the references to match our styling, refs #34371
  • lines changed 1, context: html, text, full: html, text
    9548dc8b51c2bfc8e44d8c13b2b2007a9c673317 Thu Feb 13 15:26:08 2025 -0800
    Fixing another typo, refs #34371
  • lines changed 3, context: html, text, full: html, text
    cf0ef0620d7fb30bf0d9813f8afd8fbc9c6613f9 Fri Feb 14 13:41:24 2025 -0800
    Adding a link to the CIViC website and API documentation, refs #34371
• src/hg/makeDb/trackDb/human/civic.ra
  • lines changed 1, context: html, text, full: html, text
    7036c1da9c97c601feeb085f3e39389dd5d761ab Wed Feb 12 14:06:44 2025 -0800
    CIViC: fix ClinVar links
  • lines changed 1, context: html, text, full: html, text
    9d66c3974dcd64a2f437268ba347af6fe7291d49 Thu Feb 13 15:17:58 2025 -0800
    Staging the CIViC track for hg38 and hg19 on the RR, refs #34371
• src/hg/makeDb/trackDb/human/mitoMap.html
  • lines changed 95, context: html, text, full: html, text
    2596c3765d9f8fb8ffe464d7d11ba843374f672a Wed Feb 12 12:49:11 2025 -0800
    MITOMAP track is now ready for QA, refs #24849
  • lines changed 7, context: html, text, full: html, text
    44758476f02860234fe5eb5cbf424908efa22a9a Mon Feb 17 12:25:15 2025 -0800
    Making MitoMap an otto track, refs #24849
• src/hg/makeDb/trackDb/human/mitoMap.ra
  • lines changed 35, context: html, text, full: html, text
    2596c3765d9f8fb8ffe464d7d11ba843374f672a Wed Feb 12 12:49:11 2025 -0800
    MITOMAP track is now ready for QA, refs #24849
  • lines changed 1, context: html, text, full: html, text
    44758476f02860234fe5eb5cbf424908efa22a9a Mon Feb 17 12:25:15 2025 -0800
    Making MitoMap an otto track, refs #24849
• src/hg/makeDb/trackDb/human/spliceAI.alpha.ra
  • lines changed 78, context: html, text, full: html, text
    eed605180384e7782a79dde4a364e7c82a0c647d Mon Feb 10 22:20:22 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 78, context: html, text, full: html, text
    54f66cad4f181133ae0afc8a55695adfd649e3ba Mon Feb 10 22:28:46 2025 -0800
    Revert "Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823" This reverts commit eed605180384e7782a79dde4a364e7c82a0c647d.
  • lines changed 78, context: html, text, full: html, text
    08be5093ab6c4535c129810cc78f840c5aca3c8a Thu Feb 13 14:19:52 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 5, context: html, text, full: html, text
    068989f90bc7c7497520190a753667703df3bacb Wed Feb 12 13:35:59 2025 -0800
    Revert "Turning SpliceAI into a composite instead of a superTrack so it can be nested in the splicing impact track, refs #34823" This reverts commit 0600b1ca44df66fa059b55f2357c0df6387d64b5.
• src/hg/makeDb/trackDb/human/spliceImpactSuper.alpha.ra
  • lines changed 13, context: html, text, full: html, text
    eed605180384e7782a79dde4a364e7c82a0c647d Mon Feb 10 22:20:22 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 13, context: html, text, full: html, text
    54f66cad4f181133ae0afc8a55695adfd649e3ba Mon Feb 10 22:28:46 2025 -0800
    Revert "Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823" This reverts commit eed605180384e7782a79dde4a364e7c82a0c647d.
  • lines changed 12, context: html, text, full: html, text
    08be5093ab6c4535c129810cc78f840c5aca3c8a Thu Feb 13 14:19:52 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 1, context: html, text, full: html, text
    98e34d21f00b90814efdb0a1a032b0cd0525f59c Sat Feb 15 13:49:45 2025 -0800
    add cart rewrite for the introduction of spliceImpactSuper
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
  • lines changed 4, context: html, text, full: html, text
    f4a0cd933ac7de57b77e8376123c4a14e594152a Thu Feb 6 17:02:05 2025 -0800
    Updating the SpliceVarDB methods section, refs #34424
  • lines changed 1, context: html, text, full: html, text
    623bc1182990ea8ca9c9e219906ef1a1c4a799c3 Mon Feb 10 18:07:31 2025 -0800
    Fixing longLabel for SpliceVarDB and keeping 'SpliceVarDB' string consistent in the track description page, refs #34424
• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
  • lines changed 1, context: html, text, full: html, text
    9e8e008199b18a7e418b99f246d6434d6daa72ca Mon Feb 10 17:42:56 2025 -0800
    Staging the SpliceVarDB track with the Splicing Impact super track, refs #34424
  • lines changed 1, context: html, text, full: html, text
    eed605180384e7782a79dde4a364e7c82a0c647d Mon Feb 10 22:20:22 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 1, context: html, text, full: html, text
    54f66cad4f181133ae0afc8a55695adfd649e3ba Mon Feb 10 22:28:46 2025 -0800
    Revert "Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823" This reverts commit eed605180384e7782a79dde4a364e7c82a0c647d.
  • lines changed 1, context: html, text, full: html, text
    08be5093ab6c4535c129810cc78f840c5aca3c8a Thu Feb 13 14:19:52 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
• src/hg/makeDb/trackDb/human/splicevardb.ra
  • lines changed 1, context: html, text, full: html, text
    9e8e008199b18a7e418b99f246d6434d6daa72ca Mon Feb 10 17:42:56 2025 -0800
    Staging the SpliceVarDB track with the Splicing Impact super track, refs #34424
  • lines changed 1, context: html, text, full: html, text
    623bc1182990ea8ca9c9e219906ef1a1c4a799c3 Mon Feb 10 18:07:31 2025 -0800
    Fixing longLabel for SpliceVarDB and keeping 'SpliceVarDB' string consistent in the track description page, refs #34424
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9e8e008199b18a7e418b99f246d6434d6daa72ca Mon Feb 10 17:42:56 2025 -0800
    Staging the SpliceVarDB track with the Splicing Impact super track, refs #34424
  • lines changed 4, context: html, text, full: html, text
    eed605180384e7782a79dde4a364e7c82a0c647d Mon Feb 10 22:20:22 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 4, context: html, text, full: html, text
    54f66cad4f181133ae0afc8a55695adfd649e3ba Mon Feb 10 22:28:46 2025 -0800
    Revert "Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823" This reverts commit eed605180384e7782a79dde4a364e7c82a0c647d.
  • lines changed 3, context: html, text, full: html, text
    41f433a9b05c5c98e321de75eeb9456f9d197953 Tue Feb 11 04:55:14 2025 -0800
    Updated pubtator track description
  • lines changed 2, context: html, text, full: html, text
    2596c3765d9f8fb8ffe464d7d11ba843374f672a Wed Feb 12 12:49:11 2025 -0800
    MITOMAP track is now ready for QA, refs #24849
  • lines changed 4, context: html, text, full: html, text
    08be5093ab6c4535c129810cc78f840c5aca3c8a Thu Feb 13 14:19:52 2025 -0800
    Nesting abSplice and spliceAI tracks into the spliceImpactSuper track, refs #34823
  • lines changed 1, context: html, text, full: html, text
    0cca3aec5644e9974c3154e0cb13207922055cb7 Thu Feb 13 14:26:02 2025 -0800
    Staging the CIViC track for hg38 and hg19 on hgwbeta, refs #34371
  • lines changed 1, context: html, text, full: html, text
    9d66c3974dcd64a2f437268ba347af6fe7291d49 Thu Feb 13 15:17:58 2025 -0800
    Staging the CIViC track for hg38 and hg19 on the RR, refs #34371
  • lines changed 2, context: html, text, full: html, text
    e1b63a7fd5a0b68c80498f913785b4ddf2926998 Fri Feb 14 18:48:26 2025 -0800
    Updated the pennantIcon for the Variants in Papers and the VarChat track, refs #35081
• src/hg/makeDb/trackDb/human/varChat.html
  • lines changed 29, context: html, text, full: html, text
    458c39ae52c6c4b06445115e209306357c4f923a Wed Feb 12 14:58:38 2025 -0800
    Updating the varChat description page, refs ##35081
• src/hg/utils/otto/civic/civic.as
  • lines changed 2, context: html, text, full: html, text
    7036c1da9c97c601feeb085f3e39389dd5d761ab Wed Feb 12 14:06:44 2025 -0800
    CIViC: fix ClinVar links
• src/hg/utils/otto/civic/civicToBed.py
  • lines changed 6, context: html, text, full: html, text
    155aea7ccb73e2e11ce80d93c44f7502f39ea617 Tue Feb 11 15:42:35 2025 -0800
    CIViC cancer variant track: fix DOID parsing The doid column of several tables looks a lot like a number, but many entries have leading zeroes. Pandas was reading the entire column as integer. The parsing command was changed to force the `doid` column to be treated as a string.
  • lines changed 2, context: html, text, full: html, text
    92cebf70e231042c0a994708fd8e2f850e71844a Tue Feb 11 16:04:45 2025 -0800
    CIViC variant track: disease parsing Handle any cases that may come up with disease names that include commas
  • lines changed 2, context: html, text, full: html, text
    3bbcbf1c3ac0742cafa3eb6fb2bcdfe7c51fde52 Tue Feb 11 16:06:26 2025 -0800
    CIViC variant track: disease parsing Handle any cases that may come up with disease names that include commas
• src/hg/utils/otto/clinGen/makeClinGenCspec.sh
  • lines changed 2, context: html, text, full: html, text
    8c99178b26a94e8808d87cc245ce693e0f2069f1 Thu Feb 13 09:10:46 2025 -0800
    Fixing the clinGenCspec otto that needed some continues when conditions were not met, no RM.
• src/hg/utils/otto/mitoMap/buildMitoMap.py
  • lines changed 258, context: html, text, full: html, text
    44758476f02860234fe5eb5cbf424908efa22a9a Mon Feb 17 12:25:15 2025 -0800
    Making MitoMap an otto track, refs #24849
• src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh
  • lines changed 76, context: html, text, full: html, text
    44758476f02860234fe5eb5cbf424908efa22a9a Mon Feb 17 12:25:15 2025 -0800
    Making MitoMap an otto track, refs #24849
• src/hg/utils/otto/otto.crontab
  • lines changed 3, context: html, text, full: html, text
    44758476f02860234fe5eb5cbf424908efa22a9a Mon Feb 17 12:25:15 2025 -0800
    Making MitoMap an otto track, refs #24849
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
  • lines changed 7, context: html, text, full: html, text
    4d124c77cd31a7b55284b46dd711c3354b8b78cf Wed Feb 12 17:02:00 2025 -0800
    Fixing the git compare script: removed the '\' which are not needed in the grep statement, changed the check=False in bash command to no longer error out when a find command fails, and most importantly added a check to make sure files are real (for example there were broken symlinks), and if they are real if the running user has permission to access it. No RM.
• src/inc/common.mk
  • lines changed 2, context: html, text, full: html, text
    a3dc6f427dd906f15647f68eda2fb4b75ece6ffd Mon Feb 10 15:22:59 2025 -0800
    fixed a broken makefile and so other improvements from code review
• src/inc/userApp.mk
  • lines changed 4, context: html, text, full: html, text
    a3dc6f427dd906f15647f68eda2fb4b75ece6ffd Mon Feb 10 15:22:59 2025 -0800
    fixed a broken makefile and so other improvements from code review
• src/product/README.txt
  • lines changed 4, context: html, text, full: html, text
    88bee298da706e1f201cd33de416a9159ee83a92 Wed Feb 12 12:21:56 2025 -0800
    Updating the documentation of which Linux distributions are supported for GBiC, refs #35034
• src/product/installer/README.md
  • lines changed 2, context: html, text, full: html, text
    88bee298da706e1f201cd33de416a9159ee83a92 Wed Feb 12 12:21:56 2025 -0800
    Updating the documentation of which Linux distributions are supported for GBiC, refs #35034
• src/utils/git-reports/git-reports.c
  • lines changed 7, context: html, text, full: html, text
    e42144c1f1f50cda2fb720b8586660641480a4f1 Mon Feb 10 14:59:25 2025 -0800
    Fixing git-reports for rename and copy changes, no ticket
• src/utils/hubtools/hubtools
  • lines changed 93, context: html, text, full: html, text
    2adda61e8983ceca1a9bd577c47a686a6f6990f9 Wed Feb 12 08:14:29 2025 -0800
    hubtools gets support for session links, upload, and archives, refs #34405
• src/utils/qa/assemblyStatsCron.py
  • lines changed 13, context: html, text, full: html, text
    336661f13f731c2a26a88f9acb9673f8751dac77 Fri Feb 14 08:56:56 2025 -0800
    Fixing up the monthly usage stats cron - adding a new path to the tabFmt script, and adding a cleanup step at the top of the script so that it doesn't reuse old logs if a run fails.
  • lines changed 4, context: html, text, full: html, text
    01291cd79ec246a80e79856a5c1f724d55aa39cd Fri Feb 14 11:33:30 2025 -0800
    Moving up the user var declaration, I had left it below its first use when I added the unfinished run cleanup.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    7da427db56f45ee53b29047cbe1cd2fd4df364c1 Mon Feb 17 22:17:29 2025 -0800
    v478 preview2, refs #TICKETID

• lines changed: 1769
• files changed: 111