All File Changes

v342_preview2 to v342_base (2016-11-28 to 2016-12-05) v342

• src/hg/cirm/cdw/cdwGetMetadataAsFile/cdwGetMetadataAsFile.c
  • lines changed 26, context: html, text, full: html, text
    c06583bc98841eb1fcda9b156cf97eb7926310ab Tue Nov 29 10:45:45 2016 -0800
    adding in a function to get the user data, refs #18448
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 5, context: html, text, full: html, text
    a4e458f693c542a92447564b0eedfe3422a61f58 Mon Nov 28 13:23:37 2016 -0800
    CIRM: Trying to make cdwSummary work with the new Seurat version
  • lines changed 63, context: html, text, full: html, text
    a71150f541c5d34ce4304e615dae5aa07bdd2626 Wed Nov 30 08:55:08 2016 -0800
    CIRM: fixing another Seurat issue with cdwSummary
  • lines changed 7, context: html, text, full: html, text
    b867f9efb7ae44f5ac63cbd37eaf9e8b75d9d0c2 Sat Dec 3 06:16:05 2016 -0800
    CIRM: trying work around a bug in seurat that leads to crashes on some datasets reported by Chris
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 51, context: html, text, full: html, text
    856ef21f66c0afd117faa28903595d8deb7ed21b Sun Dec 4 17:42:16 2016 -0800
    Adding metadata tree to cdwDataset page. Restricting it and file hyperlink to cases where user has permissions to access dataset.
  • lines changed 1, context: html, text, full: html, text
    48b85ae522573bc45048c5cdc3b9d04157b3c66c Sun Dec 4 17:44:28 2016 -0800
    Bumping version number.
• src/hg/cirm/cdw/cdwWebBrowse/version.doc
  • lines changed 3, context: html, text, full: html, text
    48b85ae522573bc45048c5cdc3b9d04157b3c66c Sun Dec 4 17:44:28 2016 -0800
    Bumping version number.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 21, context: html, text, full: html, text
    f5d49e1d728b1aeea2eff52761cb935dc0039ac7 Wed Nov 23 22:21:22 2016 -0800
    Making quotes in TSV quoted values be escaped by quotes as per spec, not by backslash as I assumed.
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 7, context: html, text, full: html, text
    f6aa9788d7ea71dbf2cdd8a22787700ee54a608d Sun Dec 4 17:40:19 2016 -0800
    Adding glioblastoma to disease controlled vocab, and making a new controlled vocab for fluidics_chip.
• src/hg/hgBlat/hgBlat.c
  • lines changed 3, context: html, text, full: html, text
    826153d8a963a91ca519e2dcac0c20e4793dc3e1 Mon Nov 28 12:49:38 2016 -0800
    change trash directory for blat bigPsl to "hgBlat"
  • lines changed 1, context: html, text, full: html, text
    128526c4704a9a40aa4dd26e4bdb3662c4daebb0 Mon Nov 28 17:57:25 2016 -0800
    for BLAT custom track support, call bedToBigBed in a way that disables its checking for overlapping exons, which BLAT is generating for some protein queries
  • lines changed 17, context: html, text, full: html, text
    4dd0e74f2da650f4f41ccfc29fc18df024e303d9 Tue Nov 29 18:03:37 2016 -0800
    get BLAT custom tracks to work on assembly hubs
  • lines changed 119, context: html, text, full: html, text
    e60bbad4978e2942453c6177f35cbe9291bfb930 Wed Nov 30 15:36:51 2016 -0800
    make blat custom track names conform (mostly) with the requests in #2811
• src/hg/hgGene/hgGeneData/C_elegans/links.ra
  • lines changed 1, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/links.ra
  • lines changed 1, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 1, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
  • lines changed 1, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 2, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgPal/hgPal.c
  • lines changed 1, context: html, text, full: html, text
    6ea74e3db0ef1911993bb83758b117365e5740c7 Wed Nov 30 14:45:59 2016 -0800
    change "Protein FASTA" to "Other Species FASTA" on hgGene page #18443
• src/hg/hgTracks/hgTracks.c
  • lines changed 24, context: html, text, full: html, text
    30c398a790536f060e754cbb67226d30406f6912 Wed Nov 30 12:00:52 2016 -0800
    Always put Base Position, Short Match, and Restriction Enymes tracks into group map. Make group map if it doesn't exit #16170
  • lines changed 8, context: html, text, full: html, text
    bf9606e4e09c5d48048ca399ba2cc2400d140f79 Wed Nov 30 21:54:20 2016 -0800
    adding note for keyboard shortcuts to hgTracks and documenting new zoom buttons, refs #18367
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    8469c1e45df85e202bf1f019a04a99e29722c5f4 Tue Nov 29 14:34:51 2016 -0800
    the ncbiRefSeqOther track has become a bed12 type refs #13673
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    304efa5344d37ba0f66bef4965047eff35fd3fcd Tue Nov 29 12:46:32 2016 -0800
    fix bug in "View details of alignment in window" for blat tracks that I introduced in Februrary
  • lines changed 1, context: html, text, full: html, text
    99d185b0f97224fba39b663efd48956478435450 Tue Nov 29 14:52:33 2016 -0800
    beware clicks on ncbiRefSeqOther now that it is bed12 refs #13673
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 2, context: html, text, full: html, text
    d6280afe6080d9b3c3e6b3eb0b4e3005c9411220 Mon Nov 28 12:53:53 2016 -0800
    Added changes to FAQcustom.htm pre refs #18434
  • lines changed 3, context: html, text, full: html, text
    d7e326b1887e6f764a125804b9ccf595a32d6312 Fri Dec 2 10:34:25 2016 -0800
    made changes to FAQcustom.htm per refs #18434
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 1, context: html, text, full: html, text
    89f091444a370b385e956ec8b24206533d8305ab Fri Dec 2 16:25:08 2016 -0800
    Further test trying redmine refs #18443
  • lines changed 1, context: html, text, full: html, text
    106232fb47a5c76171394a4ccc30681f142a6b8b Fri Dec 2 16:37:40 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    a91d5663e8475ebd00d5426e5f6677b9f4c679fc Fri Dec 2 16:50:43 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    35dc72d65fafdea80b4e48f498eef5386336733b Fri Dec 2 16:52:29 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    81896b6d7735d95203cb2260595f656b9f061c59 Fri Dec 2 16:53:10 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    baaf4faef2c53b5afd485351ba62e583d5d1fd45 Fri Dec 2 16:54:43 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    3f6a127ec61256dc3080c47df7e3f92c2296bd02 Fri Dec 2 16:59:10 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    8672659509d8004686e954cf044e37177015b91a Fri Dec 2 16:59:48 2016 -0800
    Further test trying redmine again refs #18443
  • lines changed 1, context: html, text, full: html, text
    66c0fea3d894c69cf60812f8b93f361a407e20fa Mon Dec 5 09:23:06 2016 -0800
    Returning wording to original state from Friday testing of redmine. By the way this has no connection with refs ##13845
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 1, context: html, text, full: html, text
    6b67d448c688375273500a79b514f55db21d24ae Fri Dec 2 16:03:16 2016 -0800
    Adding a test commit ref #13845
  • lines changed 1, context: html, text, full: html, text
    8adee0b47b2fa03b127c2d70e47f252cdfddb50f Fri Dec 2 16:18:14 2016 -0800
    Changing small word for test of RM refs #18443
  • lines changed 1, context: html, text, full: html, text
    08584cf2ab092674735b609b452678e21d367452 Fri Dec 2 16:19:43 2016 -0800
    Changing small word for test of RM refs #18443
  • lines changed 1, context: html, text, full: html, text
    0ab35e3061ea02ff69fd7d7e7bc0c816925d44f0 Fri Dec 2 16:20:39 2016 -0800
    Changing small word for test of RM refs #18443
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 4, context: html, text, full: html, text
    45fdc6a8dce8726a15caec48b9375846d402164a Tue Nov 29 11:34:03 2016 -0800
    Minor changes to gbic help page from code review, refs #18436
  • lines changed 13, context: html, text, full: html, text
    3ea8505b3e52afc9b719ddad580cdbb1acd1ba70 Fri Dec 2 07:58:40 2016 -0800
    Committing fixed gbic help file from code review, refs #18436
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    3b4b376826a1f8f2c83ce2278061b03820b4cd19 Fri Dec 2 14:12:12 2016 -0800
    Adding 2017 NAR reference, no RM
• src/hg/htdocs/training/index.html
  • lines changed 18, context: html, text, full: html, text
    f590406fad1652a44a5d08f2325518ce18f02f37 Fri Dec 2 14:28:32 2016 -0800
    adding korea and regeneron workshops
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    adadb2305d035d1b900ab1a1671e52a8b8d470a9 Mon Dec 5 10:02:47 2016 -0800
    New version number v342
• src/hg/lib/annoStreamDb.c
  • lines changed 2, context: html, text, full: html, text
    366569bbe2e738da4f223bda0a0c49fa8d6d2cef Fri Dec 2 12:24:34 2016 -0800
    Code review feedback from Kate. refs #18433
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    c73216b4e29d549efac164329f46850e5473a6c5 Fri Dec 2 17:41:47 2016 -0800
    removing an hg.conf option that could have been removed in 2007, no redmine, email from Dwayne McCully
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 1, context: html, text, full: html, text
    cddf9961aaac4513b5cdaa7273eb652f51920f16 Mon Nov 28 14:32:38 2016 -0800
    added a note to make sure that predicted mRNA sequence is all upper case in UCSC knownGene track
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 7, context: html, text, full: html, text
    c92d574a9fa6eaa51c397cae174bb1aed3ca64ec Mon Nov 28 13:20:56 2016 -0800
    Adding link to archived versions of ClinVar tracks and correcting mistakes found in CR, refs #18437 #16292
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 4, context: html, text, full: html, text
    17d3b50876f6bf1d41489df6f694178df951f5a0 Tue Nov 29 16:21:22 2016 -0800
    Updating GTEX to GTEx desc pg refs #17369
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    8469c1e45df85e202bf1f019a04a99e29722c5f4 Tue Nov 29 14:34:51 2016 -0800
    the ncbiRefSeqOther track has become a bed12 type refs #13673
  • lines changed 5, context: html, text, full: html, text
    9461ce3c12c7faa7da2480f9629a370284c54605 Tue Nov 29 15:52:54 2016 -0800
    fixing uniprot on hg38, refs #18451
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 2, context: html, text, full: html, text
    973cd9dff06f6798b551bd16eacd99f6b1387332 Tue Nov 29 10:09:37 2016 -0800
    Updating GENSAT link. Previous link was not dead, but indicated it was no longer at NCBI, refs #17323
  • lines changed 1, context: html, text, full: html, text
    ac63b72e7939e65b4c001032ecd33a72ec28cb5e Wed Nov 30 15:25:43 2016 -0800
    Updating one more link on VisiGene page, refs #17323
• src/inc/tagStorm.h
  • lines changed 17, context: html, text, full: html, text
    22ac0afac6575bd3cae4686a413a6751232b179e Sat Dec 3 11:00:27 2016 -0800
    Moving some useful tagStorm stats function to library.
• src/inc/twoBit.h
  • lines changed 3, context: html, text, full: html, text
    4dd0e74f2da650f4f41ccfc29fc18df024e303d9 Tue Nov 29 18:03:37 2016 -0800
    get BLAT custom tracks to work on assembly hubs
• src/lib/servcl.c
  • lines changed 2, context: html, text, full: html, text
    b34827e5bc4da8a6f1728693035fdec5cecc0bea Mon Nov 28 12:47:47 2016 -0800
    Kate noticed _trashDir was missing a function comment - fixed. refs #18380
• src/lib/tagStorm.c
  • lines changed 69, context: html, text, full: html, text
    22ac0afac6575bd3cae4686a413a6751232b179e Sat Dec 3 11:00:27 2016 -0800
    Moving some useful tagStorm stats function to library.
• src/lib/twoBit.c
  • lines changed 15, context: html, text, full: html, text
    4dd0e74f2da650f4f41ccfc29fc18df024e303d9 Tue Nov 29 18:03:37 2016 -0800
    get BLAT custom tracks to work on assembly hubs
• src/product/ex.hg.conf
  • lines changed 11, context: html, text, full: html, text
    92ea9d10812d61dc041ba83d118c03a00ae2eac4 Thu Dec 1 15:23:55 2016 -0800
    adding docs for two obscure hg.conf options and removing one from the gbic default file refs #18463
  • lines changed 5, context: html, text, full: html, text
    c73216b4e29d549efac164329f46850e5473a6c5 Fri Dec 2 17:41:47 2016 -0800
    removing an hg.conf option that could have been removed in 2007, no redmine, email from Dwayne McCully
• src/product/installer/README.md
  • lines changed 4, context: html, text, full: html, text
    45fdc6a8dce8726a15caec48b9375846d402164a Tue Nov 29 11:34:03 2016 -0800
    Minor changes to gbic help page from code review, refs #18436
• src/product/installer/browserSetup.sh
  • lines changed 3, context: html, text, full: html, text
    92ea9d10812d61dc041ba83d118c03a00ae2eac4 Thu Dec 1 15:23:55 2016 -0800
    adding docs for two obscure hg.conf options and removing one from the gbic default file refs #18463
• src/product/installer/docker/Dockerfile
  • lines changed 2, context: html, text, full: html, text
    a848b394a9023f90e3cc6395558b3cc1268d2c14 Sat Dec 3 06:47:35 2016 -0800
    fixing small issue with Dockerfile when running under VirtualBox, no redmine, email from Chris Lee
• src/product/mirrorDocs/staticPage.lua
  • lines changed 1, context: html, text, full: html, text
    e01ca35ad145106e1ab0f55e6a59f9b31b141437 Wed Nov 30 22:13:22 2016 -0800
    fixing TOCs for the markdown -> html converter, refs #18436
  • lines changed 11, context: html, text, full: html, text
    3eedcec63449f4c724b907e4acd58ba31b9c5a70 Thu Dec 1 14:18:35 2016 -0800
    minor change to gbic help page generator, refs #18436
• src/tagStorm/makefile
  • lines changed 1, context: html, text, full: html, text
    8b045c2c9d61baeed4bee194e68355cd85121540 Sat Dec 3 11:06:02 2016 -0800
    Adding tagStormToHtml to higher level makefile.
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 31, context: html, text, full: html, text
    dd838709307a153731b98039849a06234c8b76f9 Wed Nov 16 14:44:21 2016 -0800
    Adding vals option.
  • lines changed 1, context: html, text, full: html, text
    c279488b70255e2a20a7f8dc689889133c13c290 Wed Nov 16 14:58:43 2016 -0800
    Adding -vals option and some more test cases.
• src/tagStorm/tagStormInfo/tests/expected.counts
  • lines changed 15, context: html, text, full: html, text
    c279488b70255e2a20a7f8dc689889133c13c290 Wed Nov 16 14:58:43 2016 -0800
    Adding -vals option and some more test cases.
• src/tagStorm/tagStormInfo/tests/expected.vals
  • lines changed 41, context: html, text, full: html, text
    c279488b70255e2a20a7f8dc689889133c13c290 Wed Nov 16 14:58:43 2016 -0800
    Adding -vals option and some more test cases.
• src/tagStorm/tagStormInfo/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    c279488b70255e2a20a7f8dc689889133c13c290 Wed Nov 16 14:58:43 2016 -0800
    Adding -vals option and some more test cases.
• src/tagStorm/tagStormToHtml/makefile
  • lines changed 4, context: html, text, full: html, text
    256505d0b79d9755f767774e30767960b01868a9 Sun Dec 4 17:48:45 2016 -0800
    Oops, forgot to add makefile.
• src/tagStorm/tagStormToHtml/tagStormToHtml.c
  • lines changed 245, context: html, text, full: html, text
    681ec85f66ab8319dbe5f2656505a811cafe5924 Sat Dec 3 10:48:27 2016 -0800
    First cut of utility to turn tagStorm into a nice html page with a collapsable hierarchical list.
  • lines changed 68, context: html, text, full: html, text
    22ac0afac6575bd3cae4686a413a6751232b179e Sat Dec 3 11:00:27 2016 -0800
    Moving some useful tagStorm stats function to library.
  • lines changed 34, context: html, text, full: html, text
    ea8b346da0e42a13b4c27219467362b3eecd653f Sun Dec 4 17:39:20 2016 -0800
    Added -embed option for making code to be embedded in other pages.
• src/utils/bamToPsl/test/chr9.NM_020469.2.blat.bam
  • lines changed 0, context: html, text, full: html, text
    71745030315fee014afc06044ffdd80f161b5eea Wed Nov 30 13:46:09 2016 -0800
    adding test example refs #13673
  • lines changed 0, context: html, text, full: html, text
    a60589da31cf9a3e7ce564259f767a1ab4377eda Wed Nov 30 13:48:58 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bamToPsl/test/expectedOut.psl
  • lines changed 11, context: html, text, full: html, text
    71745030315fee014afc06044ffdd80f161b5eea Wed Nov 30 13:46:09 2016 -0800
    adding test example refs #13673
  • lines changed 11, context: html, text, full: html, text
    a60589da31cf9a3e7ce564259f767a1ab4377eda Wed Nov 30 13:48:58 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bamToPsl/test/makefile
  • lines changed 22, context: html, text, full: html, text
    71745030315fee014afc06044ffdd80f161b5eea Wed Nov 30 13:46:09 2016 -0800
    adding test example refs #13673
  • lines changed 22, context: html, text, full: html, text
    a60589da31cf9a3e7ce564259f767a1ab4377eda Wed Nov 30 13:48:58 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bamToPsl/tests/chr9.NM_020469.2.blat.bam
  • lines changed 0, context: html, text, full: html, text
    6dd72064b6370ee77e722a1ce14d0579571d6635 Wed Nov 30 13:47:56 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bamToPsl/tests/expectedOut.psl
  • lines changed 11, context: html, text, full: html, text
    6dd72064b6370ee77e722a1ce14d0579571d6635 Wed Nov 30 13:47:56 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bamToPsl/tests/makefile
  • lines changed 22, context: html, text, full: html, text
    6dd72064b6370ee77e722a1ce14d0579571d6635 Wed Nov 30 13:47:56 2016 -0800
    correct directory for tests example refs #13673
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 17, context: html, text, full: html, text
    4dd0e74f2da650f4f41ccfc29fc18df024e303d9 Tue Nov 29 18:03:37 2016 -0800
    get BLAT custom tracks to work on assembly hubs
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    ce0d81954256642dd1ecc9b11d0128422dc6239f Mon Dec 5 10:02:00 2016 -0800
    v342 final build refs #18399
• src/utils/uniprotLift
  • lines changed 69, context: html, text, full: html, text
    9461ce3c12c7faa7da2480f9629a370284c54605 Tue Nov 29 15:52:54 2016 -0800
    fixing uniprot on hg38, refs #18451
• src/utils/uniprotToTab
  • lines changed 3, context: html, text, full: html, text
    9461ce3c12c7faa7da2480f9629a370284c54605 Tue Nov 29 15:52:54 2016 -0800
    fixing uniprot on hg38, refs #18451

• lines changed: 1248
• files changed: 88