All File Changes

v391_preview to v391_preview2 (2019-11-11 to 2019-11-18) v391

• src/hg/cirm/cdw/lib/makefile
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    f6b69dbcfe28da82b1250fa1b54256812f71785e Sat Nov 16 10:16:30 2019 -0800
    fixed incorrect recursive make executions
• src/hg/expMatrixToJson/tests/makefile
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    f6b69dbcfe28da82b1250fa1b54256812f71785e Sat Nov 16 10:16:30 2019 -0800
    fixed incorrect recursive make executions
• src/hg/geneBounds/clusterGenes/clusterGenes.c
  • lines changed 5, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/joinCdsTest.gl
  • lines changed 20, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/joinTest.gl
  • lines changed 20, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/overlapIgnoreStrandsTest.gl
  • lines changed 13, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/overlapUseStrandTest.gl
  • lines changed 13, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/refSeqCdsTest.gl
  • lines changed 17, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/refSeqTest.gl
  • lines changed 17, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/geneBounds/clusterGenes/tests/expected/trackNamesTest.gl
  • lines changed 17, context: html, text, full: html, text
    06c291fd5322d86575d76d1f0f44a388371b57d7 Fri Nov 15 12:18:13 2019 -0800
    added RNA and CDS lenght to clusterGene output for easy access for post-processing
• src/hg/hgc/interactClick.c
  • lines changed 5, context: html, text, full: html, text
    7c805cc237b7cbf8d84d732c43bb4f7a394e91d6 Tue Nov 12 10:10:41 2019 -0800
    Add collapsible panel to details page when clicking on foot of interact. Requested by DanS during QA. refs #24409
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    328e57766a279798e1c9f370da17badb7cd16f6d Tue Nov 12 16:52:57 2019 -0800
    Minor proofread edits to Jonathan's Hic docs #22316
  • lines changed 30, context: html, text, full: html, text
    38c7c561433f79dd7b6a73571b4dde2e58091734 Wed Nov 13 10:30:11 2019 -0800
    Alphabetizing Hic entry #22316
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 1, context: html, text, full: html, text
    57feb7c88d4ecb6c61562ba729e2275c46e49e30 Tue Nov 12 10:11:55 2019 -0800
    Updating cse to soe subdomain no RM
• src/hg/htdocs/goldenPath/help/hgCollectionHelp.html
  • lines changed 12, context: html, text, full: html, text
    65e8a8d62a6e5441da4d02621563d6f255e92045 Fri Nov 15 13:13:24 2019 -0800
    Removing ancient starter page hgCollectionHelp.html replaced by include page: https://hgwdev.gi.ucsc.edu/inc/hgCollectionHelpInclude.html prompted by a cronjob about 404 links
• src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    328e57766a279798e1c9f370da17badb7cd16f6d Tue Nov 12 16:52:57 2019 -0800
    Minor proofread edits to Jonathan's Hic docs #22316
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 39, context: html, text, full: html, text
    328e57766a279798e1c9f370da17badb7cd16f6d Tue Nov 12 16:52:57 2019 -0800
    Minor proofread edits to Jonathan's Hic docs #22316
  • lines changed 11, context: html, text, full: html, text
    aae00b649b9a851344f98015dd192ac9b2ddc31d Wed Nov 13 13:46:22 2019 -0800
    Changing Hic citation to minimalist style refs #22316
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 277, context: html, text, full: html, text
    00b2f1735da9411ea98dc42bf7bf472aaf39052d Mon Nov 18 08:41:51 2019 -0800
    updating mirror manual, refs #24496
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 19, context: html, text, full: html, text
    e06d093f61e0fa40778a1017b997793b9207a429 Fri Nov 15 16:55:19 2019 -0800
    Changing the column.Filter nomenclature to filter.fieldName, adding filterType parameter docs, plus general refinements for filter settings refs #20227
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 4, context: html, text, full: html, text
    328e57766a279798e1c9f370da17badb7cd16f6d Tue Nov 12 16:52:57 2019 -0800
    Minor proofread edits to Jonathan's Hic docs #22316
  • lines changed 19, context: html, text, full: html, text
    e06d093f61e0fa40778a1017b997793b9207a429 Fri Nov 15 16:55:19 2019 -0800
    Changing the column.Filter nomenclature to filter.fieldName, adding filterType parameter docs, plus general refinements for filter settings refs #20227
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 104, context: html, text, full: html, text
    e06d093f61e0fa40778a1017b997793b9207a429 Fri Nov 15 16:55:19 2019 -0800
    Changing the column.Filter nomenclature to filter.fieldName, adding filterType parameter docs, plus general refinements for filter settings refs #20227
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    da0c649ca5158c447b4dc004cbfcc1eddac1203f Thu Nov 14 16:45:59 2019 -0800
    Fixing old crusty url, refs #24470
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    f32c83edb73e24c5885b787ebb67e8881087d06e Thu Nov 14 16:48:41 2019 -0800
    Adding announcement for Hi-C CT and hubs, refs #22316
• src/hg/htdocs/indexTools.html
  • lines changed 6, context: html, text, full: html, text
    d0a2f88cc0a01b5e07a856225e3dc546e64359a1 Wed Nov 13 13:10:56 2019 -0800
    Adding the REST API to the list of tools on the main page, Docs #24480
  • lines changed 6, context: html, text, full: html, text
    06891a4ae0011fb0d7981a2c22882ce538798c4c Fri Nov 15 15:31:55 2019 -0800
    Removing the hgNear CGI to have the correct number of tools on the index page, refs #24480
• src/hg/hubApi/makefile
  • lines changed 1, context: html, text, full: html, text
    f6b69dbcfe28da82b1250fa1b54256812f71785e Sat Nov 16 10:16:30 2019 -0800
    fixed incorrect recursive make executions
• src/hg/inc/bigBedFilter.h
  • lines changed 1, context: html, text, full: html, text
    87ecaf60bfa5680a064df5cea4de88abe6da22cc Wed Nov 13 19:46:43 2019 -0800
    some tweaks for filters
  • lines changed 4, context: html, text, full: html, text
    0ea39935da576d4466d1bfdcd68f84f4a7ec80e6 Thu Nov 14 14:25:23 2019 -0800
    add filterValuesDefault specification
• src/hg/inc/bigDbSnp.h
  • lines changed 1, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/hg/lib/bigDbSnp.c
  • lines changed 2, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
  • lines changed 15, context: html, text, full: html, text
    87ecaf60bfa5680a064df5cea4de88abe6da22cc Wed Nov 13 19:46:43 2019 -0800
    some tweaks for filters
  • lines changed 25, context: html, text, full: html, text
    0ea39935da576d4466d1bfdcd68f84f4a7ec80e6 Thu Nov 14 14:25:23 2019 -0800
    add filterValuesDefault specification
• src/hg/lib/jksql.c
  • lines changed 5, context: html, text, full: html, text
    ef4d994bb54291e4fa00210a4bb21fc16a53e976 Tue Nov 12 05:57:47 2019 -0800
    trying to improve error message when mysql server cannot be connected to, refs #24452
• src/hg/lib/knownIsoforms.sql
  • lines changed 1, context: html, text, full: html, text
    422154600ea64376ef82472e05379cf974b111e2 Thu Nov 14 10:27:14 2019 -0800
    add index on transcript in knownIsoforms refs #24486
• src/hg/makeDb/avada/avada.as
  • lines changed 1, context: html, text, full: html, text
    7332b44765b8b790129d59cf56b466f8d3ecb3e5 Tue Nov 12 05:22:40 2019 -0800
    fixing avada table description
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 44, context: html, text, full: html, text
    b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800
    dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
  • lines changed 17, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 44, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
  • lines changed 12, context: html, text, full: html, text
    e93b87d527fd5d292fc0dcf78ab4fc021bb9a383 Sat Nov 16 16:17:17 2019 -0800
    deleted junk accidently left in build doc
  • lines changed 1, context: html, text, full: html, text
    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 41, context: html, text, full: html, text
    2735c94211fbf200b2aaf0d349c4f5ceb74fe633 Thu Nov 14 14:48:08 2019 -0800
    hg38 finally gets 1000Genomes Phase 3 Variants, yay! refs #21805
• src/hg/makeDb/doc/mm10.txt
  • lines changed 36, context: html, text, full: html, text
    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
  • lines changed 1, context: html, text, full: html, text
    422154600ea64376ef82472e05379cf974b111e2 Thu Nov 14 10:27:14 2019 -0800
    add index on transcript in knownIsoforms refs #24486
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 8, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
  • lines changed 6, context: html, text, full: html, text
    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/schema/all.joiner
  • lines changed 97, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
  • lines changed 96, context: html, text, full: html, text
    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 3, context: html, text, full: html, text
    753af67e18c83c6480633843081d985a20f593af Thu Nov 14 08:40:17 2019 -0800
    Updating http to https for geoFor1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 10, context: html, text, full: html, text
    3d835ba54509284ec08b63dc527bd114c9467afc Tue Nov 12 10:55:41 2019 -0800
    Update counts of diffMajor, refIs{Minor,Rare,Singleton}, freqNotRefAlt after fixing VCF allele normalization in dbSnpJsonToTab. refs #23283
  • lines changed 46, context: html, text, full: html, text
    b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800
    dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
  • lines changed 16, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 104, context: html, text, full: html, text
    d3cfdd5bed4bdb1adb44e8b535e99b82d4ad6b88 Mon Nov 18 06:09:47 2019 -0800
    more children for the "special regions" tracks, refs #24245
• src/hg/makeDb/trackDb/human/hg38/tgpPhase3.html
  • lines changed 133, context: html, text, full: html, text
    2735c94211fbf200b2aaf0d349c4f5ceb74fe633 Thu Nov 14 14:48:08 2019 -0800
    hg38 finally gets 1000Genomes Phase 3 Variants, yay! refs #21805
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    2735c94211fbf200b2aaf0d349c4f5ceb74fe633 Thu Nov 14 14:48:08 2019 -0800
    hg38 finally gets 1000Genomes Phase 3 Variants, yay! refs #21805
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV33.html
  • lines changed 47, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
  • lines changed 1, context: html, text, full: html, text
    c29642913564d35b1e4953e60caadd860db99874 Sat Nov 16 16:25:48 2019 -0800
    fixed wrong version of upcomming ensembl release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV33.ra
  • lines changed 286, context: html, text, full: html, text
    4440223fad68a002964802e0ecf3b1b94cb28503 Sat Nov 16 10:11:29 2019 -0800
    import of gencode V33 prerelase
  • lines changed 6, context: html, text, full: html, text
    c29642913564d35b1e4953e60caadd860db99874 Sat Nov 16 16:25:48 2019 -0800
    fixed wrong version of upcomming ensembl release
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 45, context: html, text, full: html, text
    b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800
    dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
  • lines changed 18, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
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    fe90471e3c0b3556be22777fc6ff9ff3c0f4ea7f Thu Nov 14 11:29:24 2019 -0800
    dbSnp153Composite minor tweak: move detailsTabUrls from top level to view level. refs #23283
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    bcd29eb2ea0e1cddcc525174445423f712c9d377 Fri Nov 15 10:23:50 2019 -0800
    Typo in type declaration, doh.
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
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    9a4a058b02a66e32178f3cca85221d512de1e2e1 Tue Nov 12 11:00:43 2019 -0800
    Updating http to https for oryLat2, uiLinks cronjob.
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
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    9a4a058b02a66e32178f3cca85221d512de1e2e1 Tue Nov 12 11:00:43 2019 -0800
    Updating http to https for oryLat2, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.html
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    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.ra
  • lines changed 286, context: html, text, full: html, text
    1d8224c24263f3d0e6a418e59e86f5a8b867740f Sat Nov 16 16:51:42 2019 -0800
    import of GENCODE VM24 prerelease
• src/hg/makeDb/trackDb/worm/ce6/gap.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce6/gold.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
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    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/chainCaePb2.html
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    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
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    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/netCaeJap1.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/netCaePb2.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/netCaeRem3.html
  • lines changed 1, context: html, text, full: html, text
    c2d863d521c8263e98ea2069a0334d9a858c9a33 Mon Nov 18 08:59:43 2019 -0800
    Updating redirected links found for ce6, uiLinks cronjob.
• src/hg/snp/checkBigDbSnp/checkBigDbSnp.c
  • lines changed 65, context: html, text, full: html, text
    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 94, context: html, text, full: html, text
    b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800
    dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
• src/hg/utils/automation/doBigDbSnp.pl
  • lines changed 77, context: html, text, full: html, text
    b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800
    dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
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    54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800
    dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
• src/product/mirrorManual.txt
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    00b2f1735da9411ea98dc42bf7bf472aaf39052d Mon Nov 18 08:41:51 2019 -0800
    updating mirror manual, refs #24496
• src/utils/chromToUcsc/chromToUcsc
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    79213bd1e25c9761a4e82e1dbf00cadb9aea3672 Tue Nov 12 10:28:42 2019 -0800
    Adding additional support for different python versionds refs #24432
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
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    85c51face300add10b745269401ffbdd632fe750 Mon Nov 18 05:18:46 2019 -0800
    fixing chromToUcsc, once more, the download --get example didn't work anymore, refs #24407
• src/utils/chromToUcsc/hg19.chromAlias.tsv
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
• src/utils/chromToUcsc/hg38.chromAlias.tsv
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
• src/utils/chromToUcsc/makefile
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
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    003005fd8409969f6c109853b511afe1f3c163cb Thu Nov 14 02:13:58 2019 -0800
    changes after code review, refs #24465
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    f6b69dbcfe28da82b1250fa1b54256812f71785e Sat Nov 16 10:16:30 2019 -0800
    fixed incorrect recursive make executions
• src/utils/chromToUcsc/tests/hg19.chromAlias.tsv
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
• src/utils/chromToUcsc/tests/hg38.chromAlias.tsv
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
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    003005fd8409969f6c109853b511afe1f3c163cb Thu Nov 14 02:13:58 2019 -0800
    changes after code review, refs #24465
• src/utils/chromToUcsc/tests/makefile
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    c9e0427feeb5463fcb0a7a508a6ed3eb2480d4b4 Tue Nov 12 13:16:27 2019 +0100
    adding py2/py3 tests to chromFixer, refs #24432
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    9d1979a4f98e25cc266d29e1139dd515d11d3e61 Wed Nov 13 05:30:48 2019 -0800
    removing a feature (data stored in script itself) entirely as it was confusing, refs #24432
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    79ea010a691b96b7cc3850b87664e1ed3b266db3 Wed Nov 13 05:36:49 2019 -0800
    Removing warning message from makefile, refs #24432
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    003005fd8409969f6c109853b511afe1f3c163cb Thu Nov 14 02:13:58 2019 -0800
    changes after code review, refs #24465
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    fb4afc46f3325587835703961810e8100ef5dc4c Sat Nov 16 07:43:50 2019 -0800
    trying to eliminate " jobserver unavailable:" message from python invocation that I can't replicate
• src/utils/qa/weeklybld/buildEnv.csh
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    9b5a6a2ec22cd887b4b4e6e459e00d384f894daa Mon Nov 18 09:58:20 2019 -0800
    v391 preview2, refs #24481

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