All File Changes

v341_preview to v341_preview2 (2016-10-24 to 2016-10-31) v341

• src/hg/cirm/cdw/cdwManiFastqToKallisto/cdwManiFastqToKallisto
  • lines changed 53, context: html, text, full: html, text
    a11d63322da9a2b8c51bff01e6b9f51d3989bfb0 Fri Oct 28 15:39:15 2016 -0700
    Fixing up an error in the maniFastqToKallisto script
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 2, context: html, text, full: html, text
    14a0cd7a8f1ba71de5f44ab771aa3410651c3bbe Wed Oct 12 10:40:03 2016 -0700
    Adding metaLabelTags to cdwDataset.
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    14a0cd7a8f1ba71de5f44ab771aa3410651c3bbe Wed Oct 12 10:40:03 2016 -0700
    Adding metaLabelTags to cdwDataset.
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 13, context: html, text, full: html, text
    14a0cd7a8f1ba71de5f44ab771aa3410651c3bbe Wed Oct 12 10:40:03 2016 -0700
    Adding metaLabelTags to cdwDataset.
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 1, context: html, text, full: html, text
    14a0cd7a8f1ba71de5f44ab771aa3410651c3bbe Wed Oct 12 10:40:03 2016 -0700
    Adding metaLabelTags to cdwDataset.
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    45d3110dfcbdfbe9d0161f6cba6bab40bab24f00 Wed Oct 12 10:45:28 2016 -0700
    Adding cdwGetFile to higher level makefile
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    29ae7a228970b21ef792a9347f663d9401a6d103 Wed Oct 26 11:26:55 2016 -0700
    Adding cdwDumpManiFiles to make chain.
• src/hg/genePredCheck/genePredCheck.c
  • lines changed 14, context: html, text, full: html, text
    96442f8cb891c4f1282446f416ef9f92bc7092a1 Tue Oct 25 13:41:03 2016 -0700
    add option to genePredCheck to get chromsome sizes from file
  • lines changed 5, context: html, text, full: html, text
    983a72ac8888109a38adc922985eb110702d1af0 Wed Oct 26 14:23:12 2016 -0700
    improve usage message refs #13553
• src/hg/hgTables/intersect.c
  • lines changed 7, context: html, text, full: html, text
    a0effc171c049178f9569214bf74008ee25833a0 Thu Oct 27 11:03:48 2016 -0700
    canIntersect wasn't recognizing bigDataUrl-only tracks. refs #18289
• src/hg/hgc/mafClick.c
  • lines changed 4, context: html, text, full: html, text
    e960119647179ed6a8202f41951dc47a0d91b93c Wed Oct 26 12:12:53 2016 -0700
    weird drop-down of genePreds in mafClick wasn't setting o,t,l, or r in the cart #18283
• src/hg/hgc/vcfClick.c
  • lines changed 8, context: html, text, full: html, text
    1088a8b905852b08102668fdbb2ab9cf6d278f77 Fri Oct 28 10:10:22 2016 -0700
    Adding special code for linking out to ExAC. refs #18284
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    39d5a447ea5b3abbd5ccc9d97cf9d9b64ece4e79 Fri Oct 28 11:48:20 2016 -0700
    Woops I forgot to credit Jonathan, sorry! refs #16220
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    ca47922e02ad0cbb1cdb07238ffadd023ab1af1a Tue Oct 25 11:39:17 2016 -0700
    Adding 'darkerLabels' setting used by GTEX hubs.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
  • lines changed 5, context: html, text, full: html, text
    ca47922e02ad0cbb1cdb07238ffadd023ab1af1a Tue Oct 25 11:39:17 2016 -0700
    Adding 'darkerLabels' setting used by GTEX hubs.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 22, context: html, text, full: html, text
    ca47922e02ad0cbb1cdb07238ffadd023ab1af1a Tue Oct 25 11:39:17 2016 -0700
    Adding 'darkerLabels' setting used by GTEX hubs.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    25e10bf45bc119fa138687ba3e786185a0b1324c Wed Oct 26 15:46:27 2016 -0700
    Expanded HGVS acronym in 10-17 announcement.
  • lines changed 10, context: html, text, full: html, text
    4e9f60122280b53dd32a29ebf7303eae98b7cbc0 Wed Oct 26 15:56:23 2016 -0700
    Fixed a few grammar errors in 10-24-16 announcement.
• src/hg/inc/genePred.h
  • lines changed 6, context: html, text, full: html, text
    96442f8cb891c4f1282446f416ef9f92bc7092a1 Tue Oct 25 13:41:03 2016 -0700
    add option to genePredCheck to get chromsome sizes from file
• src/hg/lib/bigChain.as
  • lines changed 18, context: html, text, full: html, text
    9f4f2fcb80c1437130199c40a3fba71e469bda6d Thu Oct 27 13:16:04 2016 -0700
    add bigChain.as and bigLink.as to kent src
• src/hg/lib/bigLink.as
  • lines changed 12, context: html, text, full: html, text
    9f4f2fcb80c1437130199c40a3fba71e469bda6d Thu Oct 27 13:16:04 2016 -0700
    add bigChain.as and bigLink.as to kent src
• src/hg/lib/genePred.c
  • lines changed 18, context: html, text, full: html, text
    96442f8cb891c4f1282446f416ef9f92bc7092a1 Tue Oct 25 13:41:03 2016 -0700
    add option to genePredCheck to get chromsome sizes from file
• src/hg/lib/pgSnp.c
  • lines changed 114, context: html, text, full: html, text
    94699b698cc07983f2b10c5b9d4523502a4e5467 Fri Oct 28 17:18:25 2016 -0700
    Adapted from code contributed by Belinda Giardine: adding support for VCF from cancer somatic variant callers Strelka and Mutect2, when genotype columns are TUMOR and NORMAL and the hgTracks display shows allele counts for the tumor sample. For Strelka VCF, genotypes are parsed out of INFO SGT. refs #18275
• src/hg/makeDb/doc/galGal3.txt
  • lines changed 17, context: html, text, full: html, text
    47935f35970aa966bb3252ea417ada300355687d Tue Oct 25 15:19:53 2016 -0700
    per user request lift to galGal5 refs #18256
• src/hg/makeDb/doc/mm10.txt
  • lines changed 41, context: html, text, full: html, text
    242997e9231739163c33a42bf627c83b126246c0 Thu Oct 27 10:50:05 2016 -0700
    import of gencode VM10
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt
  • lines changed 230, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.allGaps.html
  • lines changed 28, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.assembly.html
  • lines changed 33, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.augustus.html
  • lines changed 106, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.build.stats.txt
  • lines changed 1, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.cpgIslands.html
  • lines changed 84, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.description.html
  • lines changed 104, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.ensGene.html
  • lines changed 30, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.gap.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.gc5Base.html
  • lines changed 21, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.names.tab
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.repeatMasker.html
  • lines changed 150, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.simpleRepeat.html
  • lines changed 48, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.windowMasker.html
  • lines changed 38, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.trackDb.txt
  • lines changed 230, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.allGaps.html
  • lines changed 28, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.assembly.html
  • lines changed 33, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.augustus.html
  • lines changed 106, context: html, text, full: html, text
    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.build.stats.txt
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.cpgIslands.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.description.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.ensGene.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.gap.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.gc5Base.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.names.tab
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.repeatMasker.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.simpleRepeat.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.windowMasker.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.trackDb.txt
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.allGaps.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.assembly.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.augustus.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.build.stats.txt
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.cpgIslands.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.description.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.ensGene.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.gap.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.gc5Base.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.names.tab
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.repeatMasker.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.simpleRepeat.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.windowMasker.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.allGaps.html
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    413ac91069f987f6c478ab0e1d5c2ef787370ee2 Mon Oct 31 09:44:20 2016 -0700
    text files for mouse strain hub hierarchy refs #13553
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    432d2039348dc0f3b12dd2f121e0b2f17bac5380 Thu Oct 27 14:00:49 2016 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    242997e9231739163c33a42bf627c83b126246c0 Thu Oct 27 10:50:05 2016 -0700
    import of gencode VM10
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM10.ra
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    242997e9231739163c33a42bf627c83b126246c0 Thu Oct 27 10:50:05 2016 -0700
    import of gencode VM10
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.html
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    242997e9231739163c33a42bf627c83b126246c0 Thu Oct 27 10:50:05 2016 -0700
    import of gencode VM10
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
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    242997e9231739163c33a42bf627c83b126246c0 Thu Oct 27 10:50:05 2016 -0700
    import of gencode VM10
• src/hg/oneShot/freen/freen.c
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    f638b0b7a16ca049e1717e2bf9da9a47874c738f Fri Oct 28 12:38:26 2016 -0700
    Freen tests sqlUnsigned
• src/hg/utils/automation/EnsGeneAutomate.pm
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    15c947622c017bc89c25268e210c9ab9b3223e01 Wed Oct 26 15:53:47 2016 -0700
    fixups to script to work on an assembly hub and fixup URL references refs #13553
• src/hg/utils/automation/asmHubAllGaps.pl
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/asmHubAugustusGene.pl
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/asmHubEnsGene.pl
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/asmHubGatewayPage.pl
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/asmHubTrackDb.sh
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/asmHubWindowMasker.pl
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    b3796b97468a12705569da8fd51d11d323225aaf Mon Oct 31 09:46:43 2016 -0700
    catch up scripts that build mouse assembly hub refs #13553
• src/hg/utils/automation/doEnsGeneUpdate.pl
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    15c947622c017bc89c25268e210c9ab9b3223e01 Wed Oct 26 15:53:47 2016 -0700
    fixups to script to work on an assembly hub and fixup URL references refs #13553
• src/hg/utils/automation/doWindowMasker.pl
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    17927a47ad8a2443fea7fd8e5a78f0e4ffbb89a3 Mon Oct 31 09:48:35 2016 -0700
    add unmaskedSeq argument to work with 2bit files not in any UCSC hierarchy refs #13553
• src/hg/utils/automation/ensGene/astMex1.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/ce11.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
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    catching up ensGene definitions refs #18240
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    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/echTel1.ensGene.ra
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    catching up ensGene definitions refs #18240
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    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/galGal5.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/hg38.ensGene.ra
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    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/lepOcu1.ensGene.ra
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    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/micMur2.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/mm10.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/ochPri2.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/oviAri3.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/papAnu2.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/poeFor1.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/pteVam1.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/rheMac8.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/rn6.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/vicPac1.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/hg/utils/automation/ensGene/xenTro3.ensGene.ra
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    0d09dbc76ff4dc88f86aca0241e7ea23b850f195 Mon Oct 31 09:59:53 2016 -0700
    catching up ensGene definitions refs #18240
• src/inc/vcf.h
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    94699b698cc07983f2b10c5b9d4523502a4e5467 Fri Oct 28 17:18:25 2016 -0700
    Adapted from code contributed by Belinda Giardine: adding support for VCF from cancer somatic variant callers Strelka and Mutect2, when genotype columns are TUMOR and NORMAL and the hgTracks display shows allele counts for the tumor sample. For Strelka VCF, genotypes are parsed out of INFO SGT. refs #18275
• src/lib/vcf.c
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    94699b698cc07983f2b10c5b9d4523502a4e5467 Fri Oct 28 17:18:25 2016 -0700
    Adapted from code contributed by Belinda Giardine: adding support for VCF from cancer somatic variant callers Strelka and Mutect2, when genotype columns are TUMOR and NORMAL and the hgTracks display shows allele counts for the tumor sample. For Strelka VCF, genotypes are parsed out of INFO SGT. refs #18275
• src/tagStorm/makefile
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    cc6e3ccad6e65acd221e70287752e2a0aef3963a Fri Oct 28 12:14:50 2016 -0700
    Adding tagStormRenameTags to higher level makefile.
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
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    4b9e005b30e32c77d49d4781176f1ff309852cb2 Fri Oct 28 12:39:10 2016 -0700
    Adding some more verbose statements to help debug.
• src/utils/qa/weeklybld/buildEnv.csh
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    v341 preview2 refs #18302

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