All File Changes

v371_preview2 to v371_base (2018-09-03 to 2018-09-10) v371

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 19, context: html, text, full: html, text
    a4483154d95553e15038edd7703dc2d6eb87437d Tue Sep 4 03:44:42 2018 -0700
    making assembly links clickable in hgHubConnect, refs #22012
  • lines changed 14, context: html, text, full: html, text
    50f54e54cab29400300ce108dc134d1645c9481b Thu Sep 6 02:27:25 2018 -0700
    suppressing clickable links for hubs that have errors in hgHubConnect, refs #22012
  • lines changed 58, context: html, text, full: html, text
    d94ba6831b6da3719ac3d6b0b28663a12df9f7b2 Fri Sep 7 02:09:38 2018 -0700
    allowing links in longer hub lists in hgHubConnect, refs #22012
  • lines changed 2, context: html, text, full: html, text
    aa3ac1d2fda0d28445c17b384b170b4b2096a561 Fri Sep 7 02:13:19 2018 -0700
    adding mouse overs to quick links on hub connect, refs #22012
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 17, context: html, text, full: html, text
    0cb4c703bd9ff662207617fa0980092ac670aece Tue Sep 4 16:52:03 2018 -0700
    add wildcard filtering and fix-up single selection in filterValue settings refs #20227
• src/hg/hgTracks/interactTrack.c
  • lines changed 7, context: html, text, full: html, text
    357f139a70677a49e14a513f1ebee31610a403a7 Sun Sep 9 14:11:16 2018 -0700
    remove some code that wasn't doing anything because the items were already filtered #22023
• src/hg/hgTracks/simpleTracks.c
  • lines changed 22, context: html, text, full: html, text
    4fa28cb0f577addf1cf9dcee723737e009afc1fd Fri Sep 7 14:23:11 2018 -0700
    add support for bigGenePred version of v29 Gencode #21644
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 7, context: html, text, full: html, text
    e93f766d2ad050342a5e41a1bc9482bcdd236dc6 Mon Sep 10 16:38:53 2018 +0200
    documenting the singleSearch hgTracks argument, no redmine
• src/hg/inc/bigBedFilter.h
  • lines changed 4, context: html, text, full: html, text
    0cb4c703bd9ff662207617fa0980092ac670aece Tue Sep 4 16:52:03 2018 -0700
    add wildcard filtering and fix-up single selection in filterValue settings refs #20227
  • lines changed 5, context: html, text, full: html, text
    d9d90603665c77c2ccdb3e1972a3dbea14c3475d Sun Sep 9 14:14:22 2018 -0700
    add some copyright messages to the tops of some files #22023
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    d0aaa83d87a554c2dd7c3816b6da0a850a7d18ee Mon Sep 10 11:13:29 2018 -0700
    New version number v371
• src/hg/lib/bigBedLabel.c
  • lines changed 4, context: html, text, full: html, text
    d9d90603665c77c2ccdb3e1972a3dbea14c3475d Sun Sep 9 14:14:22 2018 -0700
    add some copyright messages to the tops of some files #22023
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    4027e2682cacd0e0e034267b43c002421cb42314 Tue Sep 4 03:57:34 2018 -0700
    adding a small downward rectangle after the name of the view, to give an indication to the user that this is not a link but something that opens a menu below it. This is such a small change that I do not want to open a ticket for it and bother QA, so no redmine yet
  • lines changed 27, context: html, text, full: html, text
    0cb4c703bd9ff662207617fa0980092ac670aece Tue Sep 4 16:52:03 2018 -0700
    add wildcard filtering and fix-up single selection in filterValue settings refs #20227
  • lines changed 6, context: html, text, full: html, text
    739867367229d55193ca5bf94f1c271478187383 Thu Sep 6 11:17:42 2018 -0700
    only do "all or one or more" on bigBed filterBy's and fix bug #20227
  • lines changed 1, context: html, text, full: html, text
    7a760710d82d49d1322ca433317512492fe48732 Mon Sep 10 02:55:01 2018 -0700
    make sure to set the default for text matching to wildcard #20227
• src/hg/lib/variantProjector.c
  • lines changed 2, context: html, text, full: html, text
    93b4e58497bbd9a43d1fa81cc405a4c70124e806 Wed Sep 5 09:18:10 2018 -0700
    When splitting up a vpTx that spans an exon/intron junction into exon and intron components, the intron component aliBlkIx needs to be one less than the aliBlkIx of the exon to the right. refs #22029 #21979
• src/hg/lib/web.c
  • lines changed 3, context: html, text, full: html, text
    4bc6084f77a95eaacd21697240e0cf8762cec9cd Thu Sep 6 15:19:10 2018 -0700
    if db is not in URL, but genome is, use it for db #22012
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 38, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/doc/petMar1.txt
  • lines changed 27, context: html, text, full: html, text
    b325e1b53c9820126a37a6e7e12ba29d77ad5f8d Thu Sep 6 10:00:31 2018 -0700
    petMar1 to petMar3 liftOver computed refs #20819
• src/hg/makeDb/doc/wikipediaScrape.txt
  • lines changed 10, context: html, text, full: html, text
    bab1930bc04bfd2abb34eda5b78075528d06edb4 Thu Sep 6 18:44:39 2018 -0700
    scrape wikipedia for genes #21644
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 52, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/schema/all.joiner
  • lines changed 91, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/trackDb/blatHg16.html
  • lines changed 1, context: html, text, full: html, text
    e08a0efecf9ef60dd7d3b2ebf53bdd5de33134c7 Fri Sep 7 09:50:38 2018 -0700
    Updating http to https for fr1, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr1/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    e08a0efecf9ef60dd7d3b2ebf53bdd5de33134c7 Fri Sep 7 09:50:38 2018 -0700
    Updating http to https for fr1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 1, context: html, text, full: html, text
    2fa97964fc97fafcee4a9db6a9c8d95ce4a53c01 Wed Sep 5 08:54:48 2018 -0700
    Removing two pennantIcons; decipher track Jul 17th ref#21104 | GRCh37.p13 release Jul 9th ref#9869
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 5, context: html, text, full: html, text
    9cb05998ea1d3b652437eba8a9618f0279f2bf24 Thu Sep 6 08:08:53 2018 -0700
    Gencode v29 knownGene #21644
  • lines changed 1, context: html, text, full: html, text
    4fa28cb0f577addf1cf9dcee723737e009afc1fd Fri Sep 7 14:23:11 2018 -0700
    add support for bigGenePred version of v29 Gencode #21644
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 5, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV29.html
  • lines changed 47, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV29.ra
  • lines changed 285, context: html, text, full: html, text
    f50767d79e4efc238583d342dcda2a1e9d2b9094 Wed Sep 5 11:06:50 2018 -0700
    import of GENCODE V29
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2fa97964fc97fafcee4a9db6a9c8d95ce4a53c01 Wed Sep 5 08:54:48 2018 -0700
    Removing two pennantIcons; decipher track Jul 17th ref#21104 | GRCh37.p13 release Jul 9th ref#9869
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • lines changed 2, context: html, text, full: html, text
    2bddf69a5510096bb93fd161986327416b9c4ac3 Fri Sep 7 09:42:46 2018 -0700
    Updating http to https for sacCer1, uiLinks cronjob.
• src/hg/makeDb/trackDb/sacCer/sgdClone.html
  • lines changed 1, context: html, text, full: html, text
    2bddf69a5510096bb93fd161986327416b9c4ac3 Fri Sep 7 09:42:46 2018 -0700
    Updating http to https for sacCer1, uiLinks cronjob.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    9cb05998ea1d3b652437eba8a9618f0279f2bf24 Thu Sep 6 08:08:53 2018 -0700
    Gencode v29 knownGene #21644
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    66cede479f828737b4ca6d4d858b52da8a776b50 Wed Sep 5 22:23:19 2018 +0200
    fixing group for the experimental xenoClinvar track
• src/hg/rnaStructure/hgLoadRnaFold/hgLoadRnaFold.c
  • lines changed 2, context: html, text, full: html, text
    ba1364f991c175a718f2a2c853d69152ec414acb Sun Sep 9 14:15:58 2018 -0700
    remove check that was failing on recent versions of RNAfold because the sequence is now in lower case #21644
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 1, context: html, text, full: html, text
    4fa28cb0f577addf1cf9dcee723737e009afc1fd Fri Sep 7 14:23:11 2018 -0700
    add support for bigGenePred version of v29 Gencode #21644
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 5, context: html, text, full: html, text
    4b19c147c5c4bbf821aa3b97d13f78b57b3868e6 Fri Sep 7 14:01:59 2018 -0700
    If possible, use the GFF header's annotation-source value in ncbiRefSeqVersion.txt, but default to GCF_... accession if the GFF does not have annotation-source. refs #21984
• src/hg/utils/genePredToBigGenePred/makeBigKnown
  • lines changed 3, context: html, text, full: html, text
    4fa28cb0f577addf1cf9dcee723737e009afc1fd Fri Sep 7 14:23:11 2018 -0700
    add support for bigGenePred version of v29 Gencode #21644
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    d0aaa83d87a554c2dd7c3816b6da0a850a7d18ee Mon Sep 10 11:13:29 2018 -0700
    New version number v371
• src/lib/gff3.c
  • lines changed 1, context: html, text, full: html, text
    40c5c9724249bdff5eb8333acef141f20eaf7a1c Tue Sep 4 16:02:12 2018 -0700
    fixed segv when parsing invalid GFF3 header
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    45ffba376e4bbb7372d7c958ba80607f748356c5 Mon Sep 10 11:12:35 2018 -0700
    v371 final build, refs #21989
• src/utils/qa/weeklybld/preview2TablesTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    c6878a335971d5cc38942dc15e929f969f7b6886 Mon Sep 10 11:09:36 2018 -0700
    correct https reference to hgwdev.gi refs #21989

• lines changed: 791
• files changed: 45