Commits for max

v342_preview to v342_preview2 (2016-11-14 to 2016-11-28) v342

8382b726e33752590567c6dcbf834070ae51ae14 Fri Nov 11 10:15:16 2016 -0800

• making sure the clinvar otherId row can get wrapped by firefox
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 2, context: html, text, full: html, text

f5edba37a5064a01966411e3e01629d67e4983cc Tue Nov 15 00:10:59 2016 -0800

• CIRM: first go at VCF summary
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 91, context: html, text, full: html, text

907bc39d3d6aaf523023a576113f79cf24ab9e58 Tue Nov 15 00:13:58 2016 -0800

• CIRM: trying to work around missing kallisto log file data for Chris
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 7, context: html, text, full: html, text

a0d5aafda3f5ac8cff678675c715f33b9618c732 Tue Nov 15 11:33:05 2016 -0800

• CIRM: some more summary fixes, potentially related to MISCE
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 22, context: html, text, full: html, text

3711849a2a11ee46b13609e7f2a322da52a14c68 Wed Nov 16 00:22:07 2016 -0800

• fixing clinvar color problem, refs #18377
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 11, context: html, text, full: html, text

f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800

• CIRM: libifying the CDW menubar so cdwGetFile can replace <!--menuBar--> with the current menubar in html files it is serving.
  • src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c - lines changed 55, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 48, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 56, context: html, text, full: html, text

8d4d24be22066c27b2faa03b7e5ead3f303ddf93 Wed Nov 16 00:31:50 2016 -0800

• CIRM: making our menubar work with newer jquery versions needed for D3
  • src/hg/js/jquery.plugins.js - lines changed 40, context: html, text, full: html, text

b0174a409ff0f509cbdc9c26694826045083cf77 Wed Nov 16 12:59:26 2016 -0800

• adding clinvar outlinks and fixing the gene outlink bug, refs #18377
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 42, context: html, text, full: html, text
  • src/hg/utils/otto/clinvar/clinvar.as - lines changed 6, context: html, text, full: html, text

c292622618eeb59d87b5d32c7b8d4a9d95aef541 Fri Nov 18 11:43:58 2016 -0800

• CIRM: cdw summary, allowing meta file to end with .tsv instead of .tab and making sure other extensions lead to abort
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 3, context: html, text, full: html, text

07e8efc180a7d715a0a0f6d836d35ea778d4af7b Fri Nov 18 12:50:26 2016 -0800

• GBIC, adding note about missing pkgs
  • src/product/installer/browserSetup.sh - lines changed 3, context: html, text, full: html, text

86ecaa82d903eccdfb6323a9baab7f60e761ba1c Fri Nov 18 15:54:43 2016 -0800

• adding a first version of a dockerfile for the GBIC, refs #14399
  • src/product/installer/docker/Dockerfile - lines changed 18, context: html, text, full: html, text
  • src/product/installer/docker/apache.service - lines changed 21, context: html, text, full: html, text
  • src/product/installer/docker/mysql.service - lines changed 2, context: html, text, full: html, text

72e5b12d3507134b50d4b802358c8ced5f4e63a3 Fri Nov 18 15:57:34 2016 -0800

• making sure that GBIC works with Mysql 5.7 which is the default for Ubuntu 16.04
  • src/product/installer/browserSetup.sh - lines changed 8, context: html, text, full: html, text

f2784612ffb81605574914f99fd62becab52e07b Mon Nov 21 10:52:46 2016 -0800

• CIRM: allowing a manually generated summary section
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 17, context: html, text, full: html, text

66425c3d8163cb5d85e09866f165ebed0dd1a326 Mon Nov 21 14:47:21 2016 -0800

• CIRM: fix the custom track links to the genome browser to use the new "bigDataIndex" tags
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 49, context: html, text, full: html, text

59172abe9a5474b3978a897ad69d419436235984 Mon Nov 21 15:17:54 2016 -0800

• CIRM: fixing header problem
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 2, context: html, text, full: html, text

e3d3e22fd4592d4f6772efa594651ff8de791724 Mon Nov 21 15:21:29 2016 -0800

• CIRM: fixing build problem
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.h - lines changed 47, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwNavBar.h - lines changed 47, context: html, text, full: html, text

0c1d13ef4e3214c4029e098ed5ef708d15e6096f Mon Nov 21 16:34:53 2016 -0800

• CIRM: As per Jim: adding the trackDb tag 'bigDataIndex'. It allows to specify the URL of the .tbi or .bai file, in case you cannot put it alongside the .bam or .vcf.gz file.
  • src/hg/hgTracks/bamTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/vcfTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 6, context: html, text, full: html, text
  • src/inc/bamFile.h - lines changed 13, context: html, text, full: html, text
  • src/inc/linefile.h - lines changed 7, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 9, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 25, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 19, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 13, context: html, text, full: html, text

bf7071731ecf6b4b61e79786d6782326251f69c0 Mon Nov 21 16:52:55 2016 -0800

• CIRM: fixing cdwSummary bug
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 1, context: html, text, full: html, text

02177c0c71b2dd943ca6a68b5fa714c7fd9e6832 Mon Nov 21 17:02:56 2016 -0800

• CIRM: Fixing first bug in bigDataIndex handling.
  • src/hg/lib/customFactory.c - lines changed 1, context: html, text, full: html, text

3bb73cec9a7c6d0fa8ce9d919f6877e422dc13d7 Tue Nov 22 13:26:10 2016 -0800

• CIRM: redoing the support for tbi/bai index files in the CDW after having learned more about how index files are handled in the CDW.
  • src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c - lines changed 23, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 47, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 2, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 14, context: html, text, full: html, text

a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800

• adding bigDataIndex support to the table browser, refs #18420
  • src/hg/hgTables/bam.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTables/bigWig.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTables/vcf.c - lines changed 13, context: html, text, full: html, text
  • src/hg/inc/hgBam.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hgBam.c - lines changed 8, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 6, context: html, text, full: html, text

e4267cc044021c629d0b80d4ad50ec077634c3cd Tue Nov 22 16:10:57 2016 -0800

• fixing up bigDataIndex support for VCF and hgc clicks, refs #18420
  • src/hg/hgc/vcfClick.c - lines changed 4, context: html, text, full: html, text

8610c522f28515c16aed778408997136448f3c45 Wed Nov 23 05:15:16 2016 -0800

• fixing summary button for bigDataIndex support in table browser, refs #18420
  • src/hg/hgTables/bam.c - lines changed 2, context: html, text, full: html, text

459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800

• Adding VAI/DAI support for bigDataIndex, refs #18420
  • src/hg/hgVai/hgVai.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hAnno.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/hAnno.c - lines changed 21, context: html, text, full: html, text
  • src/inc/annoStreamVcf.h - lines changed 1, context: html, text, full: html, text
  • src/lib/annoStreamVcf.c - lines changed 2, context: html, text, full: html, text

60c5a57c325d324fce6072bc30b8ae859fee1030 Wed Nov 23 14:03:16 2016 -0800

• CIRM: allowing summaries without data
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 16, context: html, text, full: html, text

134d8af99fcff59e59aa0d8d807050808a11132f Wed Nov 23 14:06:07 2016 -0800

• CIRM: adding cdwSummary to main CDW makefile
  • src/hg/cirm/cdw/makefile - lines changed 1, context: html, text, full: html, text

cd635a44aa56aaa0ee3df7dbb3d099c6a7acb18f Fri Nov 25 08:51:01 2016 -0800

• fixing compile error related to bigDataIndex support
  • src/hg/lib/tests/annoGratorTester.c - lines changed 1, context: html, text, full: html, text