All File Changes

v361_base to v362_preview (2018-02-12 to 2018-02-19) v362

• confs/hgwbeta.hg.conf
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    9b6c4092bc4a05636ba92593f52ea1356d5e46c6 Sun Feb 18 01:11:46 2018 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    9b6c4092bc4a05636ba92593f52ea1356d5e46c6 Sun Feb 18 01:11:46 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwPublicSubset/cdwPublicSubset.c
  • lines changed 1, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 33, context: html, text, full: html, text
    bb6c3b94f4f2b45edc07ac62c7e68ae7d21319e6 Fri Feb 16 19:57:36 2018 -0800
    Added some images to CIP section. Added img-responsive class to some images. Added link to CESCG Seq Services PDF, no redmine
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 19, context: html, text, full: html, text
    57e82b89aecd17ae857b4d24e3ff5e84ef7b4f56 Fri Feb 16 19:55:30 2018 -0800
    Minor updates to page. Change picture for Belmonte. Add PhD for some people. Correct name misspelling. Added Hassan Chaib. no redmine
• src/hg/cirm/gateway/htdocs/images/cirmPic1.jpg
  • lines changed 0, context: html, text, full: html, text
    bb6c3b94f4f2b45edc07ac62c7e68ae7d21319e6 Fri Feb 16 19:57:36 2018 -0800
    Added some images to CIP section. Added img-responsive class to some images. Added link to CESCG Seq Services PDF, no redmine
• src/hg/cirm/gateway/htdocs/images/cirmPic2.jpg
  • lines changed 0, context: html, text, full: html, text
    bb6c3b94f4f2b45edc07ac62c7e68ae7d21319e6 Fri Feb 16 19:57:36 2018 -0800
    Added some images to CIP section. Added img-responsive class to some images. Added link to CESCG Seq Services PDF, no redmine
• src/hg/cirm/gateway/htdocs/images/cirmPic3.jpg
  • lines changed 0, context: html, text, full: html, text
    bb6c3b94f4f2b45edc07ac62c7e68ae7d21319e6 Fri Feb 16 19:57:36 2018 -0800
    Added some images to CIP section. Added img-responsive class to some images. Added link to CESCG Seq Services PDF, no redmine
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    85577a39ef899db4e859b7170e2b92b2c8d82ea2 Fri Feb 16 20:04:06 2018 -0800
    Adding img-responsive to image, no redmine
• src/hg/hgCollection/hgCollection.c
  • lines changed 1, context: html, text, full: html, text
    e9803ef31878531ce0e766f7708cd0e34c5674fc Mon Feb 12 12:29:15 2018 -0800
    fix margins on help in hgCollection
  • lines changed 6, context: html, text, full: html, text
    f33bc4bb50a4d5a8cb85729f51990c7da83613ff Fri Feb 16 17:25:19 2018 -0800
    when adding a custom track from hgTracks, change name to shortLabel, and description to longLabel
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 72, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    931b6c3eb5327760ab1ff86244bb0e03a71691e3 Wed Feb 7 17:20:51 2018 -0800
    Changing recovery email text, refs #20888
  • lines changed 2, context: html, text, full: html, text
    bcd859ab10728a7e4998c379ea76cbb7df36c7ca Wed Feb 14 12:39:18 2018 -0800
    hgLogin, fixing case where email not sent if user types in recovery email, refs #20888
• src/hg/hgTracks/pslTrack.c
  • lines changed 22, context: html, text, full: html, text
    6da76acba7f617920cc7eaa161b7d987362be78f Wed Feb 14 11:29:46 2018 -0800
    hide patent GenBank mRNA sequences by default based on accession prefix
  • lines changed 1, context: html, text, full: html, text
    4cf95232e85ac3114851417bbdc1ef9b51465761 Thu Feb 15 10:46:07 2018 -0800
    fixed typo in function names
• src/hg/hgTracks/sortWig.c
  • lines changed 16, context: html, text, full: html, text
    ee520623d0aebe293848c9005048c0e405f18f3d Fri Feb 16 14:06:05 2018 -0800
    pre-sort by name before optimal leaf sort so sort is stable
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 1, context: html, text, full: html, text
    f3fd22871e31df9c3fa9fa8dc821f048c2e952d4 Fri Feb 16 10:07:42 2018 -0800
    tiny fix to mirror manual after email from Erich, no redmine
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    e5078f0d8f2d603cefe525ca92ef832fb7f00e4b Thu Feb 15 11:17:53 2018 -0800
    Adding doWiggle note under Bam section of trackDbDoc/Hub from new trackDbLibrary addition ref #20063
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 3, context: html, text, full: html, text
    e5078f0d8f2d603cefe525ca92ef832fb7f00e4b Thu Feb 15 11:17:53 2018 -0800
    Adding doWiggle note under Bam section of trackDbDoc/Hub from new trackDbLibrary addition ref #20063
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 14, context: html, text, full: html, text
    e5078f0d8f2d603cefe525ca92ef832fb7f00e4b Thu Feb 15 11:17:53 2018 -0800
    Adding doWiggle note under Bam section of trackDbDoc/Hub from new trackDbLibrary addition ref #20063
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 121, context: html, text, full: html, text
    42cc397f8764730869873914eab8374f064888bd Fri Feb 16 10:57:29 2018 -0800
    Announcing chromAlias table for many RR assemblies, refs #20911
  • lines changed 1, context: html, text, full: html, text
    d1a8d24ad9652d042664a17d14b1a9f8849ddbb6 Fri Feb 16 11:52:48 2018 -0800
    Making a small edit to the chromAlias announcement. refs #20911
  • lines changed 23, context: html, text, full: html, text
    e7d1be0d9f2c15ddbc405d57b44f057b1f6f4fa2 Sun Feb 18 13:49:19 2018 -0800
    adding announcement of new video and link to it on training page. Also turning on links to rotterdam and san francisco workshops
  • lines changed 2, context: html, text, full: html, text
    325ebefdaae0b019dcc30ec119105eff1108b7de Sun Feb 18 16:45:45 2018 -0800
    fixed two typos
• src/hg/htdocs/images/phylo/otoGar3_3way.png
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    8cc2ddc5c3cc92e5a578423e8650684d155a53e3 Wed Feb 14 10:44:18 2018 -0800
    3-way alignment on bushbaby no redmine
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    a1231722750f05b919cd3fcf244a5431e26b2b7c Sat Feb 17 08:14:05 2018 -0800
    add hgCollection menus to top bar and hgTracks right click
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    42cc397f8764730869873914eab8374f064888bd Fri Feb 16 10:57:29 2018 -0800
    Announcing chromAlias table for many RR assemblies, refs #20911
  • lines changed 10, context: html, text, full: html, text
    e7d1be0d9f2c15ddbc405d57b44f057b1f6f4fa2 Sun Feb 18 13:49:19 2018 -0800
    adding announcement of new video and link to it on training page. Also turning on links to rotterdam and san francisco workshops
• src/hg/htdocs/style/gbStatic.css
  • lines changed 349, context: html, text, full: html, text
    afe5b077bc26b20f9c6bcf87647ba683ddfd7f48 Sat Feb 17 11:11:46 2018 -0800
    add static page css to CGI accessible location
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    be2847ec2ff93386647457cbf7c3cf295df57db7 Sat Feb 17 11:17:13 2018 -0800
    add gbStatic.css to style makefile
• src/hg/htdocs/training/index.html
  • lines changed 31, context: html, text, full: html, text
    e7d1be0d9f2c15ddbc405d57b44f057b1f6f4fa2 Sun Feb 18 13:49:19 2018 -0800
    adding announcement of new video and link to it on training page. Also turning on links to rotterdam and san francisco workshops
• src/hg/inc/genbank.h
  • lines changed 3, context: html, text, full: html, text
    6da76acba7f617920cc7eaa161b7d987362be78f Wed Feb 14 11:29:46 2018 -0800
    hide patent GenBank mRNA sequences by default based on accession prefix
  • lines changed 1, context: html, text, full: html, text
    4cf95232e85ac3114851417bbdc1ef9b51465761 Thu Feb 15 10:46:07 2018 -0800
    fixed typo in function names
• src/hg/inc/hubSearchText.h
  • lines changed 2, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    6da76acba7f617920cc7eaa161b7d987362be78f Wed Feb 14 11:29:46 2018 -0800
    hide patent GenBank mRNA sequences by default based on accession prefix
• src/hg/inc/variantProjector.h
  • lines changed 7, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
  • lines changed 2, context: html, text, full: html, text
    849d61bdaf65ea095a541f848e5af89edd85bf4a Fri Feb 16 16:06:56 2018 -0800
    Fixing outdated comment
• src/hg/js/hgTracks.js
  • lines changed 22, context: html, text, full: html, text
    a1231722750f05b919cd3fcf244a5431e26b2b7c Sat Feb 17 08:14:05 2018 -0800
    add hgCollection menus to top bar and hgTracks right click
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    cfde59a4ab19b28b93ff721d79fc3f2c13bf9405 Fri Feb 16 14:10:55 2018 -0800
    tweak validateLabel routine to require labels start with an alpha character.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 11, context: html, text, full: html, text
    0d21bf4a4674bf1e93e4db5cf51ba3053e7c7770 Thu Feb 15 13:17:13 2018 -0800
    Thanks ChrisL for noticing that HGVS g. terms were missing for intergenic variants. refs #20981
  • lines changed 2, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/lib/genbank.c
  • lines changed 42, context: html, text, full: html, text
    6da76acba7f617920cc7eaa161b7d987362be78f Wed Feb 14 11:29:46 2018 -0800
    hide patent GenBank mRNA sequences by default based on accession prefix
  • lines changed 3, context: html, text, full: html, text
    4cf95232e85ac3114851417bbdc1ef9b51465761 Thu Feb 15 10:46:07 2018 -0800
    fixed typo in function names
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/lib/hubSearchText.as
  • lines changed 1, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/lib/hubSearchText.c
  • lines changed 1, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/lib/hubSearchText.sql
  • lines changed 1, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    6da76acba7f617920cc7eaa161b7d987362be78f Wed Feb 14 11:29:46 2018 -0800
    hide patent GenBank mRNA sequences by default based on accession prefix
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    b7d662f066fea9db7d07960a403c014e079672d3 Mon Feb 12 13:33:41 2018 -0800
    allow hub.txt file to be up to 16mg instead of 256K.
• src/hg/lib/variantProjector.c
  • lines changed 59, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
  • lines changed 2, context: html, text, full: html, text
    849d61bdaf65ea095a541f848e5af89edd85bf4a Fri Feb 16 16:06:56 2018 -0800
    Fixing outdated comment
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 82, context: html, text, full: html, text
    2fc114f73975c9c559d22b8a484ab6bbc40b3d16 Tue Feb 13 09:26:02 2018 -0800
    lastz chainNet petMar3 hg38 refs #20819
• src/hg/makeDb/doc/mm10.txt
  • lines changed 74, context: html, text, full: html, text
    863a429ec3bed3f711f31f4e6604ba8adaf88412 Tue Feb 13 09:24:02 2018 -0800
    lastz chainNet petMar3 mm10 refs #20819
• src/hg/makeDb/doc/petMar3/initialBuild.txt
  • lines changed 75, context: html, text, full: html, text
    397f202b763f248f92d69d9e38426b986aadf34b Tue Feb 13 12:20:20 2018 -0800
    QA ready refs #20819
• src/hg/makeDb/doc/ucscToRefSeq.txt
  • lines changed 7, context: html, text, full: html, text
    d784a6488a4f77bf05ba405168602c96b247281a Mon Feb 12 10:23:16 2018 -0800
    indicate to check for duplicate sequences before running up idKeys refs #20913
• src/hg/makeDb/hgMergeSplitTables/hgMergeSplitTables.c
  • lines changed 1, context: html, text, full: html, text
    061bcb3ed7232ceb6438b2b583f1a6d8c535d5fb Wed Feb 14 15:55:33 2018 -0800
    Fixing sql injection issues with sqlTableLike functions in jksql.c and places that use it.
• src/hg/makeDb/schema/all.joiner
  • lines changed 14, context: html, text, full: html, text
    c21933750b24b2bec860e88050b5119d28f63a62 Mon Feb 12 15:36:35 2018 -0800
    Apply ncbiRefSeq rules to any genome database that has ncbiRefSeq tables (hopefully one day they all will, or most at least).
  • lines changed 1, context: html, text, full: html, text
    136f75919049ab512463aadf6d5ac5ec9cf59351 Thu Feb 15 14:24:33 2018 -0800
    Adding model orgs to ncbiRefSeq joiner rule, refs #20215
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
  • lines changed 413, context: html, text, full: html, text
    aad94933231615d4e48e9126c7dc493bf6ffe364 Fri Feb 16 13:14:44 2018 -0800
    3-way alignment no redmine
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    c35ed5b86fbd3b2e9c7af69ca41d8b7d4bb6b6b8 Fri Feb 16 13:19:15 2018 -0800
    fixing 4-way references to 3-way no redmine
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.3way.ra
  • lines changed 102, context: html, text, full: html, text
    aad94933231615d4e48e9126c7dc493bf6ffe364 Fri Feb 16 13:14:44 2018 -0800
    3-way alignment no redmine
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    aad94933231615d4e48e9126c7dc493bf6ffe364 Fri Feb 16 13:14:44 2018 -0800
    3-way alignment no redmine
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 1, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/encodeGencodeGeneMar07.html
  • lines changed 3, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/encodeGencodeGeneOct05.html
  • lines changed 7, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/encodeGencodeIntronOct05.html
  • lines changed 6, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/encodeGencodeRaceFrags.html
  • lines changed 1, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/consIndelsHgMmCanFam.html
  • lines changed 1, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/encodeGisChipPet.html
  • lines changed 2, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/hapmapLd.html
  • lines changed 9, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html
  • lines changed 16, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 8, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg17/retroposons.html
  • lines changed 1, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 1, context: html, text, full: html, text
    87f5709cc5f49457fcb87fe2ceb3deb2219c58a6 Tue Feb 13 11:01:29 2018 -0800
    Removing expired pennantLabels on hgTracks for cons30way and hoffMap, no RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    87f5709cc5f49457fcb87fe2ceb3deb2219c58a6 Tue Feb 13 11:01:29 2018 -0800
    Removing expired pennantLabels on hgTracks for cons30way and hoffMap, no RM
• src/hg/makeDb/trackDb/human/kiddEichlerDisc.html
  • lines changed 10, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/human/kiddEichlerValid.html
  • lines changed 10, context: html, text, full: html, text
    41c1665b86d9e8682e02a7266699e2f0bdedf3a3 Fri Feb 16 08:19:20 2018 -0800
    Fixing broken links for hg17 with more still to come. No redmine.
• src/hg/makeDb/trackDb/worm/chainCe6.html
  • lines changed 1, context: html, text, full: html, text
    bd4fdc1d169134f7aeca358783aff962e31e5a4f Wed Feb 14 08:46:49 2018 -0800
    Fixing broken links for ce6, no Redmine
• src/hg/makeDb/trackDb/worm/netCe6.html
  • lines changed 1, context: html, text, full: html, text
    bd4fdc1d169134f7aeca358783aff962e31e5a4f Wed Feb 14 08:46:49 2018 -0800
    Fixing broken links for ce6, no Redmine
• src/hg/utils/hubCrawl/hubCrawl.c
  • lines changed 13, context: html, text, full: html, text
    744a3b2e1774459ae0348822c983a24746776f96 Fri Feb 16 12:26:31 2018 -0800
    Hub text search now includes metadata tags, behaves better when encountering missing tracks/assemblies, and includes a MySQL index on the track field of hubSearchText refs #20761, #18865, #20694
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_agree.vcf
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf
  • lines changed 4, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/inc/dnautil.h
  • lines changed 3, context: html, text, full: html, text
    e9c75e7382c49565a3fae9791ab5da4f631debaa Mon Feb 12 11:02:58 2018 -0800
    In ad3a17645 I removed isAllDna from dnautil.c but not from dnautil.h - cleaned up now.
• src/product/mirrorManual.txt
  • lines changed 1, context: html, text, full: html, text
    f3fd22871e31df9c3fa9fa8dc821f048c2e952d4 Fri Feb 16 10:07:42 2018 -0800
    tiny fix to mirror manual after email from Erich, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ce0667664ca1d233595de05386e9b48cef89d50f Mon Feb 19 10:00:39 2018 -0800
    v362 preview1 refs #20889

• lines changed: 1823
• files changed: 93