File Changes for max

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

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src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
- lines changed 55, context: html, text, full: html, text
  f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
  CIRM: libifying the CDW menubar so cdwGetFile can replace  with the current menubar in html files it is serving.
- lines changed 23, 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/cdwSummary/cdwSummary
- lines changed 91, context: html, text, full: html, text
  f5edba37a5064a01966411e3e01629d67e4983cc Tue Nov 15 00:10:59 2016 -0800
  CIRM: first go at VCF summary
- lines changed 7, 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
- lines changed 22, context: html, text, full: html, text
  a0d5aafda3f5ac8cff678675c715f33b9618c732 Tue Nov 15 11:33:05 2016 -0800
  CIRM: some more summary fixes, potentially related to MISCE
- lines changed 3, 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
- lines changed 17, context: html, text, full: html, text
  f2784612ffb81605574914f99fd62becab52e07b Mon Nov 21 10:52:46 2016 -0800
  CIRM: allowing a manually generated summary section
- lines changed 1, context: html, text, full: html, text
  bf7071731ecf6b4b61e79786d6782326251f69c0 Mon Nov 21 16:52:55 2016 -0800
  CIRM: fixing cdwSummary bug
- lines changed 16, context: html, text, full: html, text
  60c5a57c325d324fce6072bc30b8ae859fee1030 Wed Nov 23 14:03:16 2016 -0800
  CIRM: allowing summaries without data
src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.h
- lines changed 47, context: html, text, full: html, text
  e3d3e22fd4592d4f6772efa594651ff8de791724 Mon Nov 21 15:21:29 2016 -0800
  CIRM: fixing build problem
src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
- lines changed 48, context: html, text, full: html, text
  f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
  CIRM: libifying the CDW menubar so cdwGetFile can replace  with the current menubar in html files it is serving.
- lines changed 49, 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
- lines changed 47, 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/inc/cdwLib.h
- lines changed 3, context: html, text, full: html, text
  f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
  CIRM: libifying the CDW menubar so cdwGetFile can replace  with the current menubar in html files it is serving.
- lines changed 2, context: html, text, full: html, text
  59172abe9a5474b3978a897ad69d419436235984 Mon Nov 21 15:17:54 2016 -0800
  CIRM: fixing header problem
- lines changed 2, 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/lib/cdwLib.c
- lines changed 56, context: html, text, full: html, text
  f587c5bc6484601bc08bab55f675cdff82d8290c Wed Nov 16 00:24:49 2016 -0800
  CIRM: libifying the CDW menubar so cdwGetFile can replace  with the current menubar in html files it is serving.
- lines changed 14, 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/lib/cdwNavBar.h
- lines changed 47, context: html, text, full: html, text
  e3d3e22fd4592d4f6772efa594651ff8de791724 Mon Nov 21 15:21:29 2016 -0800
  CIRM: fixing build problem
src/hg/cirm/cdw/makefile
- lines changed 1, context: html, text, full: html, text
  134d8af99fcff59e59aa0d8d807050808a11132f Wed Nov 23 14:06:07 2016 -0800
  CIRM: adding cdwSummary to main CDW makefile
src/hg/hgTables/bam.c
- lines changed 4, context: html, text, full: html, text
  a1dcdda03cad5b931d17066789091a64f8dceca6 Tue Nov 22 16:05:21 2016 -0800
  adding bigDataIndex support to the table browser, refs #18420
- lines changed 2, 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/bigWig.c
- lines changed 22, 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/hgTables.h
- lines changed 4, 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/vcf.c
- lines changed 13, 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/hgTracks/bamTrack.c
- lines changed 4, 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/vcfTrack.c
- lines changed 4, 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/hgVai/hgVai.c
- lines changed 6, 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/hgVarAnnogrator/hgVarAnnogrator.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/hgc/bamClick.c
- lines changed 2, 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/hgc/vcfClick.c
- lines changed 4, 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/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 6, 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/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html
- lines changed 6, 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/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 18, 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/inc/hAnno.h
- lines changed 5, 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/inc/hgBam.h
- lines changed 4, 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/js/jquery.plugins.js
- lines changed 40, 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/lib/customFactory.c
- lines changed 13, 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.
- 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/hAnno.c
- lines changed 21, 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/lib/hgBam.c
- lines changed 8, 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/lib/tests/annoGratorTester.c
- 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/utils/hubCheck/hubCheck.c
- lines changed 6, 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/utils/otto/clinvar/clinVarToBed
- lines changed 2, context: html, text, full: html, text
  8382b726e33752590567c6dcbf834070ae51ae14 Fri Nov 11 10:15:16 2016 -0800
  making sure the clinvar otherId row can get wrapped by firefox
- lines changed 11, context: html, text, full: html, text
  3711849a2a11ee46b13609e7f2a322da52a14c68 Wed Nov 16 00:22:07 2016 -0800
  fixing clinvar color problem, refs #18377
- lines changed 42, 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/clinvar.as
- lines changed 6, 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/inc/annoStreamVcf.h
- lines changed 1, context: html, text, full: html, text
  459b8273fa9eaafb16d8980567a7fcfa209fd4ef Wed Nov 23 09:30:30 2016 -0800
  Adding VAI/DAI support for bigDataIndex, refs #18420
src/inc/bamFile.h
- lines changed 13, 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/inc/linefile.h
- lines changed 7, 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/inc/vcf.h
- lines changed 9, 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/lib/annoStreamVcf.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/lib/bamFile.c
- lines changed 25, 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.
- lines changed 6, 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/lib/linefile.c
- lines changed 19, 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/lib/vcf.c
- lines changed 13, 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/product/installer/browserSetup.sh
- lines changed 3, context: html, text, full: html, text
  07e8efc180a7d715a0a0f6d836d35ea778d4af7b Fri Nov 18 12:50:26 2016 -0800
  GBIC, adding note about missing pkgs
- lines changed 8, 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/docker/Dockerfile
- lines changed 18, 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/apache.service
- lines changed 21, 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/mysql.service
- lines changed 2, 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

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