All File Changes

v354_base to v355_preview (2017-08-28 to 2017-09-04) v355

• src/hg/cirm/cdw/cdwBackup/cdwBackup
  • lines changed 10, context: html, text, full: html, text
    46922248cf1012e22c3f80d31472aa7d84be443c Mon Aug 28 14:24:10 2017 -0700
    adding cdwBackup script which gets called by cdwSubmit
• src/hg/cirm/cdw/cdwBackup/makefile
  • lines changed 9, context: html, text, full: html, text
    46922248cf1012e22c3f80d31472aa7d84be443c Mon Aug 28 14:24:10 2017 -0700
    adding cdwBackup script which gets called by cdwSubmit
  • lines changed 1, context: html, text, full: html, text
    428a50f8ce4641b966f41785f3dad9173d3a0844 Mon Aug 28 14:27:41 2017 -0700
    oops
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 7, context: html, text, full: html, text
    87e42c2812e7a93ff6c52ae5148505373d7e0c6d Wed Aug 30 15:15:14 2017 -0700
    Added advisory lock to cdwMakeFileTags so two users cannot run it at exactly the same time. If somebody else is running it, it aborts with a message explaining the conflict. Multiple users should not be running this at the same time, or it can corrupt the cdwFileTags table build.
• src/hg/cirm/cdw/makefile
  • lines changed 3, context: html, text, full: html, text
    46922248cf1012e22c3f80d31472aa7d84be443c Mon Aug 28 14:24:10 2017 -0700
    adding cdwBackup script which gets called by cdwSubmit
• src/hg/hgCollection/hgCollection.c
  • lines changed 10, context: html, text, full: html, text
    0d2757e19a4ea5280be67b8d3edcfd67ab4d01c7 Tue Aug 29 17:05:17 2017 -0700
    more updates to hgCollection
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    8d76992254bbc8ff81f73b4b48c086144a230b9e Thu Aug 31 14:58:37 2017 -0700
    fixing up some subtle html errors refs #18762
  • lines changed 6, context: html, text, full: html, text
    ceb6294adb7f7dc8e6e441a4442f01b79ef899e8 Thu Aug 31 15:07:56 2017 -0700
    encode the amp to avoid warnings from W3C validator these are URL variables refs #18762
• src/hg/hgTracks/barChartTrack.c
  • lines changed 1, context: html, text, full: html, text
    b01d5174ece9550fedb7b9c97bc94beb447f8342 Tue Aug 29 19:07:28 2017 -0700
    Seg fault protection.
• src/hg/hgTracks/gtexTracks.c
  • lines changed 1, context: html, text, full: html, text
    0a3231ebfd87922c3e0735eba832195d37dd36bf Tue Aug 29 16:42:18 2017 -0700
    A little seg-fault protection.
• src/hg/hgTracks/wigTrack.c
  • lines changed 8, context: html, text, full: html, text
    0d2757e19a4ea5280be67b8d3edcfd67ab4d01c7 Tue Aug 29 17:05:17 2017 -0700
    more updates to hgCollection
• src/hg/hgc/bigBedClick.c
  • lines changed 13, context: html, text, full: html, text
    dcb06ec7727033f47e202f2db1a0e72f0715fa73 Thu Aug 31 11:20:30 2017 -0700
    indicate no off-targets for crispr tracks when no data is available refs #20077
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    8d76992254bbc8ff81f73b4b48c086144a230b9e Thu Aug 31 14:58:37 2017 -0700
    fixing up some subtle html errors refs #18762
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 2, context: html, text, full: html, text
    004da4c12c85cf9c89bae32a8a86167f6ececf75 Mon Aug 28 13:14:18 2017 -0700
    Adding a note about two tracks in examples for wiggle.html refs #20029
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    29d650be530ef7119a5f3b2c2abd13a9e5bdcc56 Mon Aug 28 10:26:25 2017 -0700
    Fixing minor typo on newsarch, no RM
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 2, context: html, text, full: html, text
    7088b75f9316df0280ff8de64d4f793b162b56ff Fri Sep 1 10:11:44 2017 -0700
    Correcting item in item used on hgdownload per Hiram input moving LINK to head section versus body
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 57, context: html, text, full: html, text
    0d2757e19a4ea5280be67b8d3edcfd67ab4d01c7 Tue Aug 29 17:05:17 2017 -0700
    more updates to hgCollection
• src/hg/htdocs/training/index.html
  • lines changed 28, context: html, text, full: html, text
    1ceda5dcfa1b2622a42119a03355146ce7df958b Thu Aug 31 09:18:01 2017 -0700
    adding UNAM Cuernavaca workshop
  • lines changed 2, context: html, text, full: html, text
    0a808d8e22a6c39265b8fb11b8ecf9401de5cb9c Fri Sep 1 13:25:38 2017 -0700
    Adding a link to the Gene Interactions User Guide on training.html refs #18502
• src/hg/inc/jksql.h
  • lines changed 9, context: html, text, full: html, text
    87e42c2812e7a93ff6c52ae5148505373d7e0c6d Wed Aug 30 15:15:14 2017 -0700
    Added advisory lock to cdwMakeFileTags so two users cannot run it at exactly the same time. If somebody else is running it, it aborts with a message explaining the conflict. Multiple users should not be running this at the same time, or it can corrupt the cdwFileTags table build.
• src/hg/inc/variantProjector.h
  • lines changed 3, context: html, text, full: html, text
    814eddee14b8a282e9cdb1ca94e040b31cd37c12 Mon Aug 28 14:05:46 2017 -0700
    Function comment clarification.
• src/hg/inc/web.h
  • lines changed 1, context: html, text, full: html, text
    8d76992254bbc8ff81f73b4b48c086144a230b9e Thu Aug 31 14:58:37 2017 -0700
    fixing up some subtle html errors refs #18762
• src/hg/js/hgCollection.js
  • lines changed 84, context: html, text, full: html, text
    0d2757e19a4ea5280be67b8d3edcfd67ab4d01c7 Tue Aug 29 17:05:17 2017 -0700
    more updates to hgCollection
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    c80f2162ba521e6361b433497a17c67bd83d4ef7 Tue Aug 29 14:02:08 2017 -0700
    fixing highlight-off bug that must have been in the code forever, refs #20046
• src/hg/lib/barChartGeneExp.as
  • lines changed 15, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
• src/hg/lib/barChartGeneExpr.as
  • lines changed 15, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
• src/hg/lib/barChartTranscExp.as
  • lines changed 15, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
• src/hg/lib/bigBedFind.c
  • lines changed 24, context: html, text, full: html, text
    332a47e0d16a980c4d5c2edb30c0758f42949412 Wed Aug 30 12:04:17 2017 -0700
    Print out proper search description instead of table name for bigBed search result heading. Don't print out hgFindSpec search description to the right of each individual item from trix search.
  • lines changed 8, context: html, text, full: html, text
    8fc04f0d2d4ff08ea7ba0f45ec21f440140cfac2 Wed Aug 30 12:15:29 2017 -0700
    When a searchTrix file doesn't exist, warn instead of aborting with an otherwise empty page.
• src/hg/lib/hgHgvs.c
  • lines changed 13, context: html, text, full: html, text
    b5b259b8314a0253ed8c26811bb8f9167f10829d Mon Aug 28 14:11:56 2017 -0700
    hgvs{C,N}FromVpTx: when variant spans exon/intron boundary, use genomic ref instead of transcript ref so that intron bases aren't omitted. Thanks ChrisL for example in #19968-note17. refs #19968
• src/hg/lib/jksql.c
  • lines changed 45, context: html, text, full: html, text
    87e42c2812e7a93ff6c52ae5148505373d7e0c6d Wed Aug 30 15:15:14 2017 -0700
    Added advisory lock to cdwMakeFileTags so two users cannot run it at exactly the same time. If somebody else is running it, it aborts with a message explaining the conflict. Multiple users should not be running this at the same time, or it can corrupt the cdwFileTags table build.
• src/hg/lib/variantProjector.c
  • lines changed 3, context: html, text, full: html, text
    814eddee14b8a282e9cdb1ca94e040b31cd37c12 Mon Aug 28 14:05:46 2017 -0700
    Function comment clarification.
• src/hg/lib/web.c
  • lines changed 9, context: html, text, full: html, text
    8d76992254bbc8ff81f73b4b48c086144a230b9e Thu Aug 31 14:58:37 2017 -0700
    fixing up some subtle html errors refs #18762
  • lines changed 1, context: html, text, full: html, text
    b3ebe216b8706bbecf1dc7ca08e7a8ddd6b3b9a6 Thu Aug 31 15:27:58 2017 -0700
    encode the amp to avoid warnings from W3C validator these are URL variables refs #18762
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    745924e0f2b3cb897afa5fb069eba1f69d874ecd Wed Aug 30 15:50:52 2017 -0700
    Move GTex Transcript out of supertrack. A bit of cleanup. refs #19350
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 22, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
  • lines changed 2, context: html, text, full: html, text
    745924e0f2b3cb897afa5fb069eba1f69d874ecd Wed Aug 30 15:50:52 2017 -0700
    Move GTex Transcript out of supertrack. A bit of cleanup. refs #19350
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 1, context: html, text, full: html, text
    0804b0c9ab96116d3afa1a7e36710936ec6dbb60 Fri Sep 1 15:59:11 2017 -0700
    some changes I'm finally checking in after the move to a genbank machine
• src/hg/makeDb/genbank/etc/ccds-import
  • lines changed 1, context: html, text, full: html, text
    0804b0c9ab96116d3afa1a7e36710936ec6dbb60 Fri Sep 1 15:59:11 2017 -0700
    some changes I'm finally checking in after the move to a genbank machine
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    0804b0c9ab96116d3afa1a7e36710936ec6dbb60 Fri Sep 1 15:59:11 2017 -0700
    some changes I'm finally checking in after the move to a genbank machine
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • lines changed 1, context: html, text, full: html, text
    0804b0c9ab96116d3afa1a7e36710936ec6dbb60 Fri Sep 1 15:59:11 2017 -0700
    some changes I'm finally checking in after the move to a genbank machine
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    7eb22dd81e518527427204a2c5b9474402b7889f Wed Aug 30 12:05:49 2017 -0700
    Use database-specific searchTrix file for ncbiRefSeqOther.
• src/hg/makeDb/trackDb/birds/melUnd1/gap.html
  • lines changed 1, context: html, text, full: html, text
    5dae7b18e9a1d5e6155a982fdc58e0d7a89fbd56 Tue Aug 29 08:56:45 2017 -0700
    Fixing broken links found by the broken link report for melUnd1, no redmine
• src/hg/makeDb/trackDb/birds/melUnd1/gold.html
  • lines changed 1, context: html, text, full: html, text
    5dae7b18e9a1d5e6155a982fdc58e0d7a89fbd56 Tue Aug 29 08:56:45 2017 -0700
    Fixing broken links found by the broken link report for melUnd1, no redmine
• src/hg/makeDb/trackDb/blastHg17KG.html
  • lines changed 1, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/blatHg16.html
  • lines changed 2, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 4, context: html, text, full: html, text
    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
  • lines changed 1, context: html, text, full: html, text
    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 5, context: html, text, full: html, text
    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/cpgIslandSuper.html
  • lines changed 1, context: html, text, full: html, text
    5dae7b18e9a1d5e6155a982fdc58e0d7a89fbd56 Tue Aug 29 08:56:45 2017 -0700
    Fixing broken links found by the broken link report for melUnd1, no redmine
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 4, context: html, text, full: html, text
    f9d1ea7d55ff356ffab06678a2e2156512e94f87 Fri Sep 1 14:15:48 2017 -0700
    Adding documentation for the few guides that cannot be scored via Doench 2016 algorithm, refs #19874
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 6, context: html, text, full: html, text
    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
  • lines changed 6, context: html, text, full: html, text
    ba108e58038bf0eae6570f99992755e0f28fbee2 Mon Sep 4 11:21:54 2017 -0700
    Pointing to ens annotation pg instead of ens home pg, refs #19526
• src/hg/makeDb/trackDb/ensemblGeneScaffold.html
  • lines changed 5, context: html, text, full: html, text
    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/est.html
  • lines changed 9, context: html, text, full: html, text
    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/fugu/ecoresHg16.html
  • lines changed 3, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/ecoresRn3.html
  • lines changed 3, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 5, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/est.html
  • lines changed 6, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/fr1/genomicSuperDups.html
  • lines changed 2, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/gap.html
  • lines changed 2, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/intronEst.html
  • lines changed 6, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/fugu/mrna.html
  • lines changed 6, context: html, text, full: html, text
    aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700
    Fixing broken links found by the broken link report for fr1, no Redmine
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 1, context: html, text, full: html, text
    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 1, context: html, text, full: html, text
    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
  • lines changed 1, context: html, text, full: html, text
    4c5fc8b9a459abc9bc3cef56e88e4748446010a0 Fri Sep 1 08:20:28 2017 -0700
    Fixing redirected links found by the broken link report for nomLeu1, no Redmine
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
  • lines changed 1, context: html, text, full: html, text
    4c5fc8b9a459abc9bc3cef56e88e4748446010a0 Fri Sep 1 08:20:28 2017 -0700
    Fixing redirected links found by the broken link report for nomLeu1, no Redmine
• src/hg/makeDb/trackDb/human/gtexTranscExpr.html
  • lines changed 124, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
• src/hg/makeDb/trackDb/human/hg19/barCharts.ra
  • lines changed 70, context: html, text, full: html, text
    d0e2bb913b20cfd6a716ecd46d97b79add38f6cd Wed Aug 30 15:58:16 2017 -0700
    Clean up trackDb organizaion for TCGA expression tracks. refs #19155
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    54199671696f6e2616e568d69b76319beab5860d Mon Aug 28 15:55:41 2017 -0700
    Allowing hg19 to use parent ra grouping for snp tracks that also appear in hg38, no rm
• src/hg/makeDb/trackDb/human/hg19/gtexTranscExpr.html
  • lines changed 6, context: html, text, full: html, text
    426897afe49d05e59bac35a5d630352a8a3fe459 Fri Sep 1 11:26:46 2017 -0700
    Creating a shared HTML page for the GTEx Transcript track on hg19. Adding a note about how the coordinates were converted from hg38 to hg19. refs #19350
• src/hg/makeDb/trackDb/human/hg19/gtexTranscriptExpression.html
  • lines changed 119, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
• src/hg/makeDb/trackDb/human/hg19/snpedia.html
  • lines changed 38, context: html, text, full: html, text
    b18baf9c5fe52cb6541285f2d4377a04a4c6be10 Fri Sep 1 16:40:08 2017 -0700
    Snpedia update, refs #19811
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    0a92935c0b74f6f0cd13f8bc60cdfd4a02146bca Mon Aug 28 14:03:47 2017 -0700
    working on variation group ordering, no rm
  • lines changed 6, context: html, text, full: html, text
    54199671696f6e2616e568d69b76319beab5860d Mon Aug 28 15:55:41 2017 -0700
    Allowing hg19 to use parent ra grouping for snp tracks that also appear in hg38, no rm
  • lines changed 3, context: html, text, full: html, text
    745924e0f2b3cb897afa5fb069eba1f69d874ecd Wed Aug 30 15:50:52 2017 -0700
    Move GTex Transcript out of supertrack. A bit of cleanup. refs #19350
  • lines changed 12, context: html, text, full: html, text
    139c29ad49ee56b190785fc3e82a750d11e98136 Wed Aug 30 15:52:20 2017 -0700
    Fix merge conflict
  • lines changed 2, context: html, text, full: html, text
    f9597814417dbbe5140f65db7ffcabf909ae475d Wed Aug 30 15:59:55 2017 -0700
    Clean up trackDb organizaion for GTEx transcript track. refs #19350
  • lines changed 1, context: html, text, full: html, text
    426897afe49d05e59bac35a5d630352a8a3fe459 Fri Sep 1 11:26:46 2017 -0700
    Creating a shared HTML page for the GTEx Transcript track on hg19. Adding a note about how the coordinates were converted from hg38 to hg19. refs #19350
  • lines changed 12, context: html, text, full: html, text
    b18baf9c5fe52cb6541285f2d4377a04a4c6be10 Fri Sep 1 16:40:08 2017 -0700
    Snpedia update, refs #19811
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    54199671696f6e2616e568d69b76319beab5860d Mon Aug 28 15:55:41 2017 -0700
    Allowing hg19 to use parent ra grouping for snp tracks that also appear in hg38, no rm
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 1, context: html, text, full: html, text
    54199671696f6e2616e568d69b76319beab5860d Mon Aug 28 15:55:41 2017 -0700
    Allowing hg19 to use parent ra grouping for snp tracks that also appear in hg38, no rm
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
  • lines changed 150, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
  • lines changed 154, context: html, text, full: html, text
    139c29ad49ee56b190785fc3e82a750d11e98136 Wed Aug 30 15:52:20 2017 -0700
    Fix merge conflict
  • lines changed 154, context: html, text, full: html, text
    35faac6076ca61915d5e79dd70c264949ab54bb2 Wed Aug 30 15:55:27 2017 -0700
    Clean up trackDb organizaion for TCGA expression tracks. refs #19155
• src/hg/makeDb/trackDb/human/hg38/cancerExpr.ra
  • lines changed 60, context: html, text, full: html, text
    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
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    4dd567c3f268de962aa1109cd5f479c33ca6004e Wed Aug 30 19:35:39 2017 -0700
    Sticking with supertrack for now (composite close to working but not quite). refs #19155
• src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html
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    051454361d9ccc0e51168697741c74caa1cc6048 Mon Aug 28 17:15:40 2017 -0700
    Minor doc cleanup. refs #19350
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    f1f8d705c60c02d1c66a32f26ab7d334cf338d6f Thu Aug 31 10:32:01 2017 -0700
    Adding a link to the Toil home page, refs #19350
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    1c3a1fba24adfb8092672478fa99ced539d125c4 Thu Aug 31 10:49:06 2017 -0700
    Replacing single quotes with double quotes for HTML attributes, refs #19350
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    0a9933520f41643aef5ee2f5eb7eed00d5fa3e7b Thu Aug 31 11:13:43 2017 -0700
    Adding spacing to the barchart image, refs #19350
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    989ab541a5249d80d2625247880a0fd22f38cd6a Thu Aug 31 11:29:03 2017 -0700
    Italicizing our tools, refs #19350
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    a22be5d8fb33bbb0f91a315694f4ee29767e2f0e Thu Aug 31 11:57:41 2017 -0700
    Updating broken and redirected links, refs #19350
• src/hg/makeDb/trackDb/human/hg38/gtexTranscriptExpression.html
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    051454361d9ccc0e51168697741c74caa1cc6048 Mon Aug 28 17:15:40 2017 -0700
    Minor doc cleanup. refs #19350
• src/hg/makeDb/trackDb/human/hg38/tcgaExpr.html
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    42e1ceff3c233348062964c8048dfe137dcf5d94 Tue Aug 29 16:26:28 2017 -0700
    Adding a missing period, CR #20054
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    91d315a30eaf630a5b92ac4c7c525676cde96248 Wed Aug 30 15:28:03 2017 -0700
    Reorg TCGA gene expression tracks as a composite. refs #19155
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    745924e0f2b3cb897afa5fb069eba1f69d874ecd Wed Aug 30 15:50:52 2017 -0700
    Move GTex Transcript out of supertrack. A bit of cleanup. refs #19350
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    139c29ad49ee56b190785fc3e82a750d11e98136 Wed Aug 30 15:52:20 2017 -0700
    Fix merge conflict
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    436d5324a97236c1121faf2ae3b590871ed980d6 Wed Aug 30 15:56:17 2017 -0700
    Clean up trackDb organizaion for TCGA expression tracks. refs #19155
• src/hg/makeDb/trackDb/human/snpedia.html
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    b18baf9c5fe52cb6541285f2d4377a04a4c6be10 Fri Sep 1 16:40:08 2017 -0700
    Snpedia update, refs #19811
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    745924e0f2b3cb897afa5fb069eba1f69d874ecd Wed Aug 30 15:50:52 2017 -0700
    Move GTex Transcript out of supertrack. A bit of cleanup. refs #19350
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    de9afc71920dc3812b5da527cab189d9ffefb8cf Wed Aug 30 19:36:14 2017 -0700
    Tweak priority so GTEx tracks are together. refs #19350
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    93d5103daee27501d0aad87753ac52f69ceba551 Thu Aug 31 16:02:46 2017 -0700
    Adding a maxItems limit to prevent loading issues, refs #19350
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    bb3e4008901303e6ad9c131380ede5cfdd2c9c37 Fri Sep 1 15:10:00 2017 -0700
    Adding the beta release tag to stage the GTEx Transcript Expression on hgwbeta, refs #19350
• src/hg/makeDb/trackDb/human/trackDb.ra
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    0a92935c0b74f6f0cd13f8bc60cdfd4a02146bca Mon Aug 28 14:03:47 2017 -0700
    working on variation group ordering, no rm
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    54199671696f6e2616e568d69b76319beab5860d Mon Aug 28 15:55:41 2017 -0700
    Allowing hg19 to use parent ra grouping for snp tracks that also appear in hg38, no rm
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    b18baf9c5fe52cb6541285f2d4377a04a4c6be10 Fri Sep 1 16:40:08 2017 -0700
    Snpedia update, refs #19811
• src/hg/makeDb/trackDb/intronEst.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/medaka/oryLat2/ctgPos2.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/mrna.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/nestedRepeats.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/nscanGene.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/pubs.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/pubsBingBlat.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/refGene.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    7eb22dd81e518527427204a2c5b9474402b7889f Wed Aug 30 12:05:49 2017 -0700
    Use database-specific searchTrix file for ncbiRefSeqOther.
• src/hg/makeDb/trackDb/rmsk.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/tRNAs.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/tagTypes.tab
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    625931e8a4276fe7d803413e5a9e93e881263439 Thu Aug 31 10:20:06 2017 -0700
    add gtexTranscExpr to types that can have bigDataUrl
• src/hg/makeDb/trackDb/transMap.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/transMapAlnMRna.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/transMapAlnRefSeq.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
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    14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700
    Fixing broken links found by the broken link report for felCat3, no Redmine
• src/hg/makeDb/trackDb/transMapTailer.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/ucscToINSDC.html
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    5dae7b18e9a1d5e6155a982fdc58e0d7a89fbd56 Tue Aug 29 08:56:45 2017 -0700
    Fixing broken links found by the broken link report for melUnd1, no redmine
• src/hg/makeDb/trackDb/windowmaskerSdust.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/makeDb/trackDb/xenoMrna.html
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    c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700
    Fixing broken links found by the broken link report for oryLat2, no redmine
• src/hg/pslCheck/pslCheck.c
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    87160c4c6abc63ea1732458d5b58ca8bd420528c Wed Aug 30 08:53:24 2017 -0700
    added option to pslCheck to not check insert sizes
• src/hg/utils/automation/gbffToCds.pl
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    c471518148d5f26876f8baa94c7b9ac6bdf6056a Thu Aug 31 14:15:28 2017 -0700
    catch up missing script refs #13673
• src/hg/utils/automation/grcRunIncidentUpdate.sh
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    003597c6660eb96664f03683ef17ab3005e658d1 Wed Aug 30 17:51:11 2017 -0700
    hg38 updates to p11 and mm10 to p5 refs #16660
• src/hg/utils/vcfToHgvs/tests/PGTdb/chromAlias.tab
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/chromInfo.tab
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeq.gp.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqCds.tab.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqLink.tab.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqPepTable.tab.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/ncbiRefSeqPsl.psl.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/PGTdb/seqNcbiRefSeq.rna.fa.gz
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab
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    b5b259b8314a0253ed8c26811bb8f9167f10829d Mon Aug 28 14:11:56 2017 -0700
    hgvs{C,N}FromVpTx: when variant spans exon/intron boundary, use genomic ref instead of transcript ref so that intron bases aren't omitted. Thanks ChrisL for example in #19968-note17. refs #19968
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
• src/hg/utils/vcfToHgvs/tests/makefile
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    556daa1b7d9c0fdf4a4ea184fd4b3dfcca00ccce Thu Aug 31 11:53:37 2017 -0700
    Added stable test data for vcfToHgvs's "Personalis Ground Truth" test set, to avoid nightly build test errors caused by regular RefSeq updates. Instead of trying to recreate a subset of refGene/genbank tables and files, I'm using the ncbiRefSeq* schema since it is much more self-contained. In order to reduce the test set size a bit, I excluded some alternate transcripts whose HGVS terms weren't very different from the primary transcripts. The tests/expected/Personalis* files changed instead of simply shrinking because now the transcript acc column includes version number because that's the ncbiRefSeq way. The hg38 stopLoss test might conceivably change someday in an ncbiRefSeq update -- but that should be rare enough that I don't think it's worth the effort and git bloat to make stable test data for it at this point.
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    4317d66f127eb7d193d9f464e3889279e5c58d9d Fri Sep 1 08:52:33 2017 -0700
    Doh, forgot to use -f in clean target rm... rm -f, rm -f, rm -f.
• src/inc/common.mk
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    3840f06abae2ec4a7a37e83a3533bc53efaae36e Fri Sep 1 12:32:03 2017 -0700
    now using libpng.a and libz.a need to reorder link libs and add some for Mac OSX build refs #9149
• src/inc/psl.h
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    87160c4c6abc63ea1732458d5b58ca8bd420528c Wed Aug 30 08:53:24 2017 -0700
    added option to pslCheck to not check insert sizes
• src/lib/cosmicNew.as
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    3a8c011a50a167d8777ce6286456eefd558c77c4 Tue Aug 29 09:36:37 2017 -0700
    remove duplicate copy of cosmicNew.as
• src/lib/dnaseq.c
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    3d7b476fc7a80bb445107cf2f6cdfd10070f4321 Mon Aug 28 14:07:40 2017 -0700
    Use pointer subtraction instead of strlen, HT Braney in code review, refs #19992
• src/lib/htmshell.c
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    7ea47ecdd280f60036477a2c9774004cf129a690 Thu Aug 31 14:03:14 2017 -0700
    empty ul list is illegal, add an empty item refs #18762
• src/lib/psl.c
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    87160c4c6abc63ea1732458d5b58ca8bd420528c Wed Aug 30 08:53:24 2017 -0700
    added option to pslCheck to not check insert sizes
• src/makefile
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    f9a754afcc53c42a6918be835a8328f8f80dcf2a Fri Sep 1 11:55:13 2017 -0700
    for userApps build test directories exist before using them refs #9149
• src/userApps/README
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    aef39ab54a651136d06d8f25ecda204df710ff03 Fri Sep 1 11:00:13 2017 -0700
    note new dependent library libuuid-devel requirement refs #9149
• src/utils/makefile
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    bc172b659b426818b82e185e9846aa63b2a9544d Tue Aug 29 09:53:44 2017 -0700
    CIRM: new tool webSync, a small script that can download hundreds of thousands of files quickly from a webserver and keep them in sync with a local directory. Like rsync, but faster and does not require an open port.
• src/utils/qa/weeklybld/buildEnv.csh
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    f51051af30f72958f252438d91a72295462b2f24 Mon Sep 4 11:39:44 2017 -0700
    running up v355 preview1 refs #19997
• src/utils/webSync
  • lines changed 268, context: html, text, full: html, text
    bc172b659b426818b82e185e9846aa63b2a9544d Tue Aug 29 09:53:44 2017 -0700
    CIRM: new tool webSync, a small script that can download hundreds of thousands of files quickly from a webserver and keep them in sync with a local directory. Like rsync, but faster and does not require an open port.

• lines changed: 3079
• files changed: 158