All File Changes

v373_preview2 to v373_base (2018-10-15 to 2018-10-22) v373

• confs/hgwbeta.hg.conf
  • lines changed 5, context: html, text, full: html, text
    93ee4b3fe41393630408afa1d55f09383be04a48 Sun Oct 21 01:11:33 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    93ee4b3fe41393630408afa1d55f09383be04a48 Sun Oct 21 01:11:33 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 4, context: html, text, full: html, text
    93ee4b3fe41393630408afa1d55f09383be04a48 Sun Oct 21 01:11:33 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 2, context: html, text, full: html, text
    b045e19c74f5bf4eaab3bfd451012c907682c684 Mon Oct 15 23:15:12 2018 -0700
    Making cdwMakeEnrichments ignore csv and tsv files rather than erroring out on them.
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 6, context: html, text, full: html, text
    1da5a55f7e10a60f92aa8d1af943792175af2a4f Mon Oct 15 23:14:13 2018 -0700
    Adding some verboseTime statements to help profiling.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 35, context: html, text, full: html, text
    4f7a6a707c428acd6a4455a36fc219a762394f03 Mon Oct 15 23:01:39 2018 -0700
    Bumping version number. Stripping out test page code. Speeding up browse datasets page.
  • lines changed 109, context: html, text, full: html, text
    e4ce7704c86148dfc44f96a43a49f997443ed37e Fri Oct 19 12:10:11 2018 -0700
    Replacing cdwWebBrowse analysisQuery handling with something faster, refs #21693
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 5, context: html, text, full: html, text
    4f7a6a707c428acd6a4455a36fc219a762394f03 Mon Oct 15 23:01:39 2018 -0700
    Bumping version number. Stripping out test page code. Speeding up browse datasets page.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 4, context: html, text, full: html, text
    e4ce7704c86148dfc44f96a43a49f997443ed37e Fri Oct 19 12:10:11 2018 -0700
    Replacing cdwWebBrowse analysisQuery handling with something faster, refs #21693
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 1, context: html, text, full: html, text
    384330b5616f204176489c2ef91b1244e18f2945 Mon Oct 15 23:06:32 2018 -0700
    Adding comment about a slow query.
  • lines changed 76, context: html, text, full: html, text
    e4ce7704c86148dfc44f96a43a49f997443ed37e Fri Oct 19 12:10:11 2018 -0700
    Replacing cdwWebBrowse analysisQuery handling with something faster, refs #21693
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 7, context: html, text, full: html, text
    cf56b6dcd5aa3a2bd0994211c3539862f400ead6 Mon Oct 15 23:12:42 2018 -0700
    Fixing a few missing bits on supporting 2bit, customTrack, and expression_matrix formats.
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 2, context: html, text, full: html, text
    cf5882f73c47fd710e697ff8e2ee1c1ee0527504 Mon Oct 15 14:38:09 2018 -0700
    Commenting out line for Clarke lab. no redmine
• src/hg/hgBlat/hgBlat.c
  • lines changed 83, context: html, text, full: html, text
    c4f23aaa36169fc4ee7aa14c7fb0eaf69bfb7a02 Thu Oct 18 18:13:40 2018 -0700
    Adding support to hgBlat for searching attached hubs gfServers
• src/hg/hgTracks/barChartTrack.c
  • lines changed 3, context: html, text, full: html, text
    2c2c9f2efae8089d434f53693cbf4bb564a5c32b Fri Oct 19 10:10:17 2018 -0700
    Fixing display bug when no barChart items arein view, found by Dan, refs #18508
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    ce8ecbbd267e3cd3f1c9bb24ace346e61fbe9019 Thu Oct 18 11:27:36 2018 -0700
    Fix some issues with linked features display (tall region). refs #21917
• src/hg/hgTracks/interactTrack.c
  • lines changed 31, context: html, text, full: html, text
    ce8ecbbd267e3cd3f1c9bb24ace346e61fbe9019 Thu Oct 18 11:27:36 2018 -0700
    Fix some issues with linked features display (tall region). refs #21917
• src/hg/hgTracks/simpleTracks.c
  • lines changed 14, context: html, text, full: html, text
    ce8ecbbd267e3cd3f1c9bb24ace346e61fbe9019 Thu Oct 18 11:27:36 2018 -0700
    Fix some issues with linked features display (tall region). refs #21917
• src/hg/hgc/gencodeClick.c
  • lines changed 6, context: html, text, full: html, text
    94c06184a32f9465b63c0dc812d8914e0993127e Mon Oct 15 13:21:03 2018 -0700
    fixed link to APPRIS server (#21852)
• src/hg/hgc/interactClick.c
  • lines changed 86, context: html, text, full: html, text
    a44c8fabb2a8c93192e32a3fc125bc9f2775d623 Wed Oct 17 14:45:41 2018 -0700
    Fixes to cluster mode, click through on 'foot' in curve display (handling of multiple hits). refs #21917
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 94, context: html, text, full: html, text
    498fc94c93d87ac77d5c34d4b36f01eeb701b7ce Fri Oct 19 11:48:57 2018 -0700
    updating documentation for BLAT ALL, refs #18992
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 54, context: html, text, full: html, text
    d6c5f9aa1a341eb47d7d0d7cfa56d06f43c8754d Wed Oct 17 16:45:50 2018 -0700
    Cleaned up examples and updated button labels ref#22035
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 11, context: html, text, full: html, text
    498fc94c93d87ac77d5c34d4b36f01eeb701b7ce Fri Oct 19 11:48:57 2018 -0700
    updating documentation for BLAT ALL, refs #18992
• src/hg/htdocs/indexTools.html
  • lines changed 1, context: html, text, full: html, text
    68a85b436e9ceca3c05e8dbe5a91ebf6f3bf99ee Thu Oct 18 15:35:57 2018 -0700
    better URL, per Brian Lee's code review, refs #22258
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    c66f3aa17c73ef4818516700180e50ffffad0e30 Mon Oct 22 10:09:03 2018 -0700
    New version number v373
• src/hg/lib/hgHgvs.c
  • lines changed 2, context: html, text, full: html, text
    54d8983c10eaff12d0e287b09f6417f7c37bcdf5 Tue Oct 16 13:24:24 2018 -0700
    Oops, forgot to call normalizeVersion in hgvsToTxCoords to get consistent RefSeq vs. GenBank transcript CDS. 'make test' failure triggered by GenBank update.
• src/hg/makeDb/doc/galGal6/initialBuild.txt
  • lines changed 86, context: html, text, full: html, text
    a6734a481a1a646dfc51ea62e2661cfb3d159e18 Wed Oct 17 09:50:31 2018 -0700
    QA ready refs #22113
• src/hg/makeDb/doc/galGal6/lastzProcedures.txt
  • lines changed 73, context: html, text, full: html, text
    fe83e2d25c4a88169fc720c4ea28134e9f65e430 Mon Oct 22 09:56:58 2018 -0700
    document the parasol procedures refs #22113
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
  • lines changed 3900, context: html, text, full: html, text
    6e84c8dc5d24b4e9acc51741ac2543d087e00dc8 Mon Oct 22 09:37:28 2018 -0700
    document the lastz/chain/net alignments refs #22113
• src/hg/makeDb/doc/galGal6/prepOne.pl
  • lines changed 151, context: html, text, full: html, text
    fe83e2d25c4a88169fc720c4ea28134e9f65e430 Mon Oct 22 09:56:58 2018 -0700
    document the parasol procedures refs #22113
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh
  • lines changed 14, context: html, text, full: html, text
    a01b107255b3a595185467973c49b74af01d9c3e Fri Oct 19 15:26:42 2018 -0700
    some ucsc genes fixes #21644
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    909a19d1d1c1f1fdde8bb58c453b066a60053895 Mon Oct 15 13:46:39 2018 -0700
    Added galGal6 - chicken refs #22113
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    6631ff5b82f1a08eab3d99752631d35201d51216 Tue Oct 16 13:21:22 2018 -0700
    galGal6 does not yet have ensembl transcripts refs #22113
  • lines changed 6, context: html, text, full: html, text
    d41898db9c0022520a3bfef5b3655f56e2d1c80b Fri Oct 19 10:33:32 2018 -0700
    Adding all.joiner rules for updated rmskJoined tracks, refs #18273
  • lines changed 7, context: html, text, full: html, text
    a01b107255b3a595185467973c49b74af01d9c3e Fri Oct 19 15:26:42 2018 -0700
    some ucsc genes fixes #21644
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    64ce04359d8c3719ea2c6d1685ab348c14044bec Fri Oct 19 08:49:44 2018 -0700
    Updating http to https for geoFor1, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetBirds.ra
  • lines changed 882, context: html, text, full: html, text
    6ae2c01d76ce418f94d49ca30296e461b3c6bcc4 Sun Oct 21 22:14:25 2018 -0700
    initial look at the 77-way alignments refs #22113
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetFish.ra
  • lines changed 178, context: html, text, full: html, text
    6ae2c01d76ce418f94d49ca30296e461b3c6bcc4 Sun Oct 21 22:14:25 2018 -0700
    initial look at the 77-way alignments refs #22113
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetvertebrate.ra
  • lines changed 290, context: html, text, full: html, text
    6ae2c01d76ce418f94d49ca30296e461b3c6bcc4 Sun Oct 21 22:14:25 2018 -0700
    initial look at the 77-way alignments refs #22113
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    8b8ba4a483d34b37d51759f6c119cddc490bec59 Tue Oct 16 18:59:38 2018 -0700
    adding crispr 10K track refs #22113
  • lines changed 4, context: html, text, full: html, text
    6ae2c01d76ce418f94d49ca30296e461b3c6bcc4 Sun Oct 21 22:14:25 2018 -0700
    initial look at the 77-way alignments refs #22113
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 9, context: html, text, full: html, text
    86123f99c3a1cad21d0a584c151a0426ad574ed5 Wed Oct 17 17:15:30 2018 -0700
    Sanitize email address. refs #21917
  • lines changed 12, context: html, text, full: html, text
    feab0b9547becb8b50f5dd79561f49e84871e92e Wed Oct 17 17:25:51 2018 -0700
    Add links to methods section. refs #21917
  • lines changed 1, context: html, text, full: html, text
    79b7acf240e9661aa08121d26705f7963edba7d0 Wed Oct 17 17:27:04 2018 -0700
    Remove errant superscript. refs #21917
• src/hg/makeDb/trackDb/joinedRmsk.html
  • lines changed 5, context: html, text, full: html, text
    080a11060de3c916270f6654270e5fe0b0de008a Fri Oct 19 16:04:51 2018 -0700
    joinedRmsk.html punctuation update
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 4, context: html, text, full: html, text
    3213be5bee060670fa7c1f340c9c7ee753da205a Tue Oct 16 11:53:06 2018 -0700
    Updating http to https for petMar1, uiLinks cronjob.
• src/hg/makeDb/trackDb/lamprey/petMar1/phastConsElements6way.html
  • lines changed 4, context: html, text, full: html, text
    3213be5bee060670fa7c1f340c9c7ee753da205a Tue Oct 16 11:53:06 2018 -0700
    Updating http to https for petMar1, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM16.ra
  • lines changed 2, context: html, text, full: html, text
    d11ff15efeda22afc405d5ec83bd3bcd07b3a329 Mon Oct 15 13:39:43 2018 -0700
    turning VM16 to hide, refs #21852
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 36, context: html, text, full: html, text
    628408f6e74ddc9a50bab828507fb4c210691fb1 Wed Oct 17 14:12:40 2018 -0700
    adding ncbiRefSeqDiff to description page, refs#21079
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 4, context: html, text, full: html, text
    5dc85cf958d42a7478eeb079719003a776a697d2 Tue Oct 16 12:07:38 2018 -0700
    correctly honor the trackHub argument even if dbExists refs #18874
• src/hg/utils/automation/doCrispr.pl
  • lines changed 54, context: html, text, full: html, text
    ffac66398e499bf14aca0ff0dc2521797dae670d Mon Oct 15 14:36:48 2018 -0700
    add indexFa step for new genome sequence and add /dev/shm/ setup with the fasta and its index for kluster nodes refs #22113
  • lines changed 57, context: html, text, full: html, text
    0ed07b82cb5cb138e7157e885607ba32dca71660 Wed Oct 17 10:32:33 2018 -0700
    adding cleanup procedure refs #22113
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 2, context: html, text, full: html, text
    5dc85cf958d42a7478eeb079719003a776a697d2 Tue Oct 16 12:07:38 2018 -0700
    correctly honor the trackHub argument even if dbExists refs #18874
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    88af4cb287894068f2c49013a1c79fd8ed9bea3a Mon Oct 15 11:38:09 2018 -0700
    Added library to get HAL integration to link. Not sure why this worked for others
• src/inc/rql.h
  • lines changed 4, context: html, text, full: html, text
    33b6fd1ac519b70e12f061ac052e50253e00aae7 Wed Oct 17 16:59:53 2018 -0700
    Adding rqlToSql library to convert RQL into SQL statements, no ticket
• src/inc/rqlToSql.h
  • lines changed 19, context: html, text, full: html, text
    33b6fd1ac519b70e12f061ac052e50253e00aae7 Wed Oct 17 16:59:53 2018 -0700
    Adding rqlToSql library to convert RQL into SQL statements, no ticket
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    c66f3aa17c73ef4818516700180e50ffffad0e30 Mon Oct 22 10:09:03 2018 -0700
    New version number v373
• src/inc/udc.h
  • lines changed 13, context: html, text, full: html, text
    09243c7da5f14dbfa408cf7a54e567080da81a05 Wed Oct 17 10:44:15 2018 -0700
    Added ability to access UDC file in cache using virtual memory (mmap). The test sure are nice.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    33b6fd1ac519b70e12f061ac052e50253e00aae7 Wed Oct 17 16:59:53 2018 -0700
    Adding rqlToSql library to convert RQL into SQL statements, no ticket
• src/lib/rqlParse.c
  • lines changed 2, context: html, text, full: html, text
    7a68eb7d4da510a798a22fe6cf258f8385c29269 Wed Oct 17 14:31:24 2018 -0700
    Fix for rqlParseDump crashing on array nodes, refs #22286
• src/lib/rqlToSql.c
  • lines changed 166, context: html, text, full: html, text
    33b6fd1ac519b70e12f061ac052e50253e00aae7 Wed Oct 17 16:59:53 2018 -0700
    Adding rqlToSql library to convert RQL into SQL statements, no ticket
• src/lib/tests/udcTest.c
  • lines changed 23, context: html, text, full: html, text
    09243c7da5f14dbfa408cf7a54e567080da81a05 Wed Oct 17 10:44:15 2018 -0700
    Added ability to access UDC file in cache using virtual memory (mmap). The test sure are nice.
• src/lib/udc.c
  • lines changed 36, context: html, text, full: html, text
    09243c7da5f14dbfa408cf7a54e567080da81a05 Wed Oct 17 10:44:15 2018 -0700
    Added ability to access UDC file in cache using virtual memory (mmap). The test sure are nice.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 5, context: html, text, full: html, text
    926f508a32a3fdc5ce8bcebc8491e1634e48bd83 Mon Oct 22 10:08:15 2018 -0700
    v373 final build, refs #22231

• lines changed: 6709
• files changed: 64