All File Changes

v336_preview2 to v336_base (2016-07-18 to 2016-07-25) v336

• confs/hgwdev.hg.conf
  • lines changed 7, context: html, text, full: html, text
    357c0a0d0bd0e945a68c5b2f3f81b6f026f28838 Sun Jul 24 01:11:57 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/browserbox/makefile
  • lines changed 4, context: html, text, full: html, text
    b0b0150d8733c01c3bc94ca21abd1e152fa5ca57 Thu Jul 21 12:25:22 2016 -0700
    adding cram support to gbib, refs #17547
    
• src/browserbox/root/fetchCramReference.sh
  • lines changed 112, context: html, text, full: html, text
    b0b0150d8733c01c3bc94ca21abd1e152fa5ca57 Thu Jul 21 12:25:22 2016 -0700
    adding cram support to gbib, refs #17547
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 15, context: html, text, full: html, text
    b0b0150d8733c01c3bc94ca21abd1e152fa5ca57 Thu Jul 21 12:25:22 2016 -0700
    adding cram support to gbib, refs #17547
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 11, context: html, text, full: html, text
    b0b0150d8733c01c3bc94ca21abd1e152fa5ca57 Thu Jul 21 12:25:22 2016 -0700
    adding cram support to gbib, refs #17547
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 6, context: html, text, full: html, text
    1f2603cbaeb38d6e465a8cfdde8fef88e751b5f1 Fri Jul 8 07:18:47 2016 -0700
    Passing assay into a library function for a new trimming step.
    
  • lines changed 4, context: html, text, full: html, text
    e03dc8b59d956f25ff3c2617ffaf60c57a23be8b Fri Jul 8 10:54:30 2016 -0700
    Fixing up the cutadapt call, need a .fastq before the .gz, which is done now with a symbolic link
    
• src/hg/cirm/cdw/cdwManiFastqToKallisto/cdwManiFastqToKallisto
  • lines changed 191, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/cdwManiFastqToKallisto/makefile
  • lines changed 6, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 26, context: html, text, full: html, text
    3b1d0cf233b3e801f1cc07fa52813ad06562938a Fri Jul 8 07:19:19 2016 -0700
    Putting a cutadapt call into the pipeline for longRNASeq data types.
    
  • lines changed 11, context: html, text, full: html, text
    e03dc8b59d956f25ff3c2617ffaf60c57a23be8b Fri Jul 8 10:54:30 2016 -0700
    Fixing up the cutadapt call, need a .fastq before the .gz, which is done now with a symbolic link
    
  • lines changed 77, context: html, text, full: html, text
    e40e0ad96f119b8756b92a8cf483d6869773acc3 Wed Jul 13 09:58:19 2016 -0700
    Adding in a cutadapt step to remove poly A tails which were gunking up the pipeline at the BWA step, refs #17334
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 191, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/makefile
  • lines changed 6, context: html, text, full: html, text
    72a82b6b2c77ad9e364ed002e5fb306e25a41cd0 Fri Jul 1 13:38:58 2016 -0700
    renaming this script and moving it to a more appropriate directory, refs #16244
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 10, context: html, text, full: html, text
    f1b861623af3f6c4ec36c745db34c3a72438ff9f Tue Jul 19 09:21:12 2016 -0700
    Added new hg.conf setting surveyLabelImage -- if present, then hgGateway will display an <img> with the setting value as src to the right of the GO button. refs #17622
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 2, context: html, text, full: html, text
    f1b861623af3f6c4ec36c745db34c3a72438ff9f Tue Jul 19 09:21:12 2016 -0700
    Added new hg.conf setting surveyLabelImage -- if present, then hgGateway will display an <img> with the setting value as src to the right of the GO button. refs #17622
    
• src/hg/hgTables/bam.c
  • lines changed 19, context: html, text, full: html, text
    69e65f45d0db6e87a72aa22c5aa61c3c4f6f2412 Mon Jul 18 14:33:48 2016 -0700
    fix up some problems in table browser with CRAM output #17698
    
• src/hg/hgTables/bigWig.c
  • lines changed 2, context: html, text, full: html, text
    69e65f45d0db6e87a72aa22c5aa61c3c4f6f2412 Mon Jul 18 14:33:48 2016 -0700
    fix up some problems in table browser with CRAM output #17698
    
• src/hg/hgc/hgc.c
  • lines changed 34, context: html, text, full: html, text
    9c25510eb2cbb183c4e630d3519c693d33672dec Mon Jul 18 16:59:07 2016 -0700
    dbSNP includes some deletions >1kbp so just clone the reference allele instead of trying to copy into finite-size char[]. However, abbreviate really long alleles for display so they don't mess up the page. refs #10937.
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    94c208fbd61206036632029fc7101b25c7d24f2c Mon Jul 18 15:58:00 2016 -0700
    Removed class that prevented POST links to genome-store as it's no longer needed, refs #17703
    
• src/hg/htdocs/makefile
  • lines changed 2, context: html, text, full: html, text
    27cef4cf0721d13c97d4ef15032ea7cc63dc3fa7 Thu Jul 21 08:37:56 2016 -0700
    Spelling corrections as per code review, refs #17727
    
• src/hg/htdocs/pandoc/installer/makefile
  • lines changed 2, context: html, text, full: html, text
    27cef4cf0721d13c97d4ef15032ea7cc63dc3fa7 Thu Jul 21 08:37:56 2016 -0700
    Spelling corrections as per code review, refs #17727
    
• src/hg/htdocs/style/jWest.css
  • lines changed 6, context: html, text, full: html, text
    f1b861623af3f6c4ec36c745db34c3a72438ff9f Tue Jul 19 09:21:12 2016 -0700
    Added new hg.conf setting surveyLabelImage -- if present, then hgGateway will display an <img> with the setting value as src to the right of the GO button. refs #17622
    
• src/hg/htdocs/training/index.html
  • lines changed 7, context: html, text, full: html, text
    b310b12449ddae0e804305489ad5f0e9d90f784b Thu Jul 21 12:07:08 2016 -0700
    adding ucsf workshop
    
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    f41b7312f74139ab5b5580d6767d12b456c831d7 Thu Jul 21 17:45:59 2016 -0700
    remove the canDoCoverage hg.conf variable.
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    9267845b10041f488a126bbf7475d800b2a4f330 Mon Jul 25 10:42:27 2016 -0700
    New version number v336
    
• src/hg/js/hgGateway.js
  • lines changed 10, context: html, text, full: html, text
    f1b861623af3f6c4ec36c745db34c3a72438ff9f Tue Jul 19 09:21:12 2016 -0700
    Added new hg.conf setting surveyLabelImage -- if present, then hgGateway will display an <img> with the setting value as src to the right of the GO button. refs #17622
    
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    f41b7312f74139ab5b5580d6767d12b456c831d7 Thu Jul 21 17:45:59 2016 -0700
    remove the canDoCoverage hg.conf variable.
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 37, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/doc/hg38/uniprot.txt
  • lines changed 28, context: html, text, full: html, text
    273486dcbd4a0fd80d7f09be639f32cd58598881 Wed Jul 20 15:03:46 2016 -0700
    adding uniprot track for hg38
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 40, context: html, text, full: html, text
    8ed64ae893841ce58ce790c1a557008d6a229612 Sat Jul 23 05:39:33 2016 -0700
    load of GENCODE VM10
    
  • lines changed 2, context: html, text, full: html, text
    b3b5fd99de3eebac7a61f47b2cd8953580380a8b Sat Jul 23 07:04:01 2016 -0700
    update joiner check for GENCODE VM10
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    1f015787fc2ebc3d47e40962372204cdd24378af Thu Jul 21 13:19:15 2016 -0700
    turning on genbank updates for galVar1, refs #17180
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 7, context: html, text, full: html, text
    8ed64ae893841ce58ce790c1a557008d6a229612 Sat Jul 23 05:39:33 2016 -0700
    load of GENCODE VM10
    
  • lines changed 5, context: html, text, full: html, text
    040df170f551f086894ca532fc1472d7cd2eb684 Sat Jul 23 05:50:49 2016 -0700
    forgotten update of gencode VM10 tags
    
  • lines changed 2, context: html, text, full: html, text
    b3b5fd99de3eebac7a61f47b2cd8953580380a8b Sat Jul 23 07:04:01 2016 -0700
    update joiner check for GENCODE VM10
    
  • lines changed 9, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 85, context: html, text, full: html, text
    b3b5fd99de3eebac7a61f47b2cd8953580380a8b Sat Jul 23 07:04:01 2016 -0700
    update joiner check for GENCODE VM10
    
  • lines changed 91, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 23, context: html, text, full: html, text
    b9ad4adc4a2872033c7aaad1dfed5e1be0c71875 Thu Jul 21 12:26:09 2016 -0700
    adding data section to clinvar (no redmine) and pointer to uniprot hub
    to uniprot track refs #17717
    
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.ra
  • lines changed 2, context: html, text, full: html, text
    722417f79bae84e88d3da9d1e73828c7d9452809 Mon Jul 18 16:05:53 2016 -0700
    Small spelling change to short and long label of gencode v22 and v23
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.ra
  • lines changed 2, context: html, text, full: html, text
    722417f79bae84e88d3da9d1e73828c7d9452809 Mon Jul 18 16:05:53 2016 -0700
    Small spelling change to short and long label of gencode v22 and v23
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.html
  • lines changed 368, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.ra
  • lines changed 274, context: html, text, full: html, text
    6c700418f3dfa9b5ecf84bb6491693b7fa88ba0c Sat Jul 23 11:40:26 2016 -0700
    load of GENCODE V25
    
• src/hg/makeDb/trackDb/human/snp147.shared.html
  • lines changed 4, context: html, text, full: html, text
    c4c31faa727a72ddc3c63301a4341ba8b4a7527f Thu Jul 21 12:00:34 2016 -0700
    Escaping a couple special chars, refs #17209
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
  • lines changed 1, context: html, text, full: html, text
    8ed64ae893841ce58ce790c1a557008d6a229612 Sat Jul 23 05:39:33 2016 -0700
    load of GENCODE VM10
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM10.html
  • lines changed 343, context: html, text, full: html, text
    8ed64ae893841ce58ce790c1a557008d6a229612 Sat Jul 23 05:39:33 2016 -0700
    load of GENCODE VM10
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM10.ra
  • lines changed 272, context: html, text, full: html, text
    8ed64ae893841ce58ce790c1a557008d6a229612 Sat Jul 23 05:39:33 2016 -0700
    load of GENCODE VM10
    
  • lines changed 2, context: html, text, full: html, text
    040df170f551f086894ca532fc1472d7cd2eb684 Sat Jul 23 05:50:49 2016 -0700
    forgotten update of gencode VM10 tags
    
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/spUniprot.html
  • lines changed 22, context: html, text, full: html, text
    273486dcbd4a0fd80d7f09be639f32cd58598881 Wed Jul 20 15:03:46 2016 -0700
    adding uniprot track for hg38
    
  • lines changed 6, context: html, text, full: html, text
    b9ad4adc4a2872033c7aaad1dfed5e1be0c71875 Thu Jul 21 12:26:09 2016 -0700
    adding data section to clinvar (no redmine) and pointer to uniprot hub
    to uniprot track refs #17717
    
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 1, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/makeDb/trackDb/zebrafish/danRer2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    5896c6c1fe9d479aad89bd5fa9f6903193503646 Mon Jul 18 12:34:40 2016 -0700
    change refLink to hgFixed.refLink in trackDb
    
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 124, context: html, text, full: html, text
    3b64b7ab91f935d1327852681029ab24a484ea72 Thu Jul 21 23:36:47 2016 -0700
    running up windowMasker and cpgIslands tracks refs #13553
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 4, context: html, text, full: html, text
    05f5763fe041c89acbeed0dfb1c267d55b586223 Fri Jul 22 10:30:29 2016 -0700
    Added chmods to dbSNP download files so that others don't run into permissions errors (thx Jonathan) refs #16847
    
• src/hg/utils/automation/genbank/assemblyDescription.pl
  • lines changed 2, context: html, text, full: html, text
    5fa4407a8c8d49d13806c2d21bdd59b8feae4848 Fri Jul 22 14:25:57 2016 -0700
    Updating links to assembly and AGP help pages at NCBI, refs #17114
    
• src/hg/utils/automation/genbank/gapDescription.pl
  • lines changed 2, context: html, text, full: html, text
    5fa4407a8c8d49d13806c2d21bdd59b8feae4848 Fri Jul 22 14:25:57 2016 -0700
    Updating links to assembly and AGP help pages at NCBI, refs #17114
    
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    5fa4407a8c8d49d13806c2d21bdd59b8feae4848 Fri Jul 22 14:25:57 2016 -0700
    Updating links to assembly and AGP help pages at NCBI, refs #17114
    
• src/product/installer/README.md
  • lines changed 10, context: html, text, full: html, text
    ff4c778d071a33d91ef897e1eb59526e2a83ac7c Thu Jul 21 15:54:37 2016 -0700
    Bolding titles and fixing typos as per code review, refs #17727
    
  • lines changed 1, context: html, text, full: html, text
    3d1a59e76bdcd9ef01738c5c65fd631918f31f96 Mon Jul 25 10:34:46 2016 -0700
    typo in README
    
• src/product/scripts/fetchCramReference.sh
  • lines changed 3, context: html, text, full: html, text
    fa44dd7153c4904ab3e7d3fb6c4d4aeb0943fdc1 Thu Jul 21 10:19:57 2016 -0700
    small fixed to the cram fetching script, refs #17547
    
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    2845759e8b8bf4950755ca1a1270ecd60abaa19b Tue Jul 19 12:34:57 2016 -0700
    adding an AWK script that Mark wrote. I am using this script for the
    uniprot track and am comitting it now so that the uniprot pipeline can
    be run
    
  • lines changed 2, context: html, text, full: html, text
    273486dcbd4a0fd80d7f09be639f32cd58598881 Wed Jul 20 15:03:46 2016 -0700
    adding uniprot track for hg38
    
• src/utils/pslProtCnv
  • lines changed 65, context: html, text, full: html, text
    2845759e8b8bf4950755ca1a1270ecd60abaa19b Tue Jul 19 12:34:57 2016 -0700
    adding an AWK script that Mark wrote. I am using this script for the
    uniprot track and am comitting it now so that the uniprot pipeline can
    be run
    
• src/utils/pslSameGene
  • lines changed 54, context: html, text, full: html, text
    273486dcbd4a0fd80d7f09be639f32cd58598881 Wed Jul 20 15:03:46 2016 -0700
    adding uniprot track for hg38
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    691dfdc3a3b9fa84794086bd862d97e2eb85738f Mon Jul 25 10:41:24 2016 -0700
    v336 final build
    
• src/utils/uniprotLift
  • lines changed 4, context: html, text, full: html, text
    273486dcbd4a0fd80d7f09be639f32cd58598881 Wed Jul 20 15:03:46 2016 -0700
    adding uniprot track for hg38
    
• src/utils/uniprotToTab
  • lines changed 12, context: html, text, full: html, text
    745524a7cc8f2fb4bceea120fd25201ddeff6acc Tue Jul 19 13:39:08 2016 -0700
    fixing an issue where uniprotToTab would not work with trembl. Email
    from Eric Ho, refs #17717
    

• lines changed: 2713
• files changed: 75