All File Changes

v338_preview to v338_preview2 (2016-08-22 to 2016-08-29) v338

• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    244125ce6c458ee8f030f221af2928e6c9cabe7b Sun Aug 28 01:11:39 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 1, context: html, text, full: html, text
    f92cd3e0ca317d5ce7720accce00fdb29f794959 Mon Aug 22 14:26:24 2016 -0700
    removing a select * and putting in select named fields which lead to a
    bug in the cdwSummary pages.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 91, context: html, text, full: html, text
    f9a299037436cb6ddae4e551d2ec2952a45a35f9 Thu Aug 25 12:32:07 2016 -0700
    Refactoring the code for speed, refs #17870
    
• src/hg/hgGene/gtex.c
  • lines changed 5, context: html, text, full: html, text
    13d5f7b0d091ed228affad0262face3167f00d2e Wed Aug 24 14:52:52 2016 -0700
    Gene page link to browser from GTEx section now includes gene position, so if launched from other than browser (e.g. Gene Sorter) it will show gene region. refs #17288
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 44, context: html, text, full: html, text
    5a63b70b7e8405a187c8fba71c557cca655e0424 Wed Aug 24 12:17:38 2016 -0700
    Add config option to display ENS geneId. For synergy with new GTEx gene sorter column. refs #17288
    
• src/hg/hgc/gtexClick.c
  • lines changed 2, context: html, text, full: html, text
    293923a610a014d169a8b4c83a3d91719aab942c Wed Aug 24 14:54:08 2016 -0700
    Comment out broken link to GTEx portal. Broad has been alerted.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 6, context: html, text, full: html, text
    78706245dcc5a52cef38bd7daf496c811df17330 Thu Aug 25 14:34:40 2016 -0700
    Minor changes to PSL protein query section, refs #17662
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 11, context: html, text, full: html, text
    608e714bfeec249d8be71f4fa3e5115e25d338e0 Wed Aug 24 09:34:21 2016 -0700
    updated html so all example links in #SHARE section open in new tab, refs #14591
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    0621b2d2e8177660a528d70503133658e21928c1 Wed Aug 24 09:52:40 2016 -0700
    adding info from url to url_for_hubs in trackDb doc
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 12, context: html, text, full: html, text
    37d4c8acbdce252710aa78453e0bcdbbe3641cb9 Fri Aug 26 16:10:16 2016 -0700
    Adding Max's CRISPOR paper to our pubs page
    
• src/hg/inc/gtexUi.h
  • lines changed 7, context: html, text, full: html, text
    5a63b70b7e8405a187c8fba71c557cca655e0424 Wed Aug 24 12:17:38 2016 -0700
    Add config option to display ENS geneId. For synergy with new GTEx gene sorter column. refs #17288
    
• src/hg/inc/pslReader.h
  • lines changed 5, context: html, text, full: html, text
    370394fc362cce1b14f32e1a9d548fd5654063a0 Tue Aug 23 09:59:15 2016 -0700
    Account for bin column when loading estOrientInfo data.
    Add function to read selected PSLs from a table into memory.
    
• src/hg/inc/soTerm.h
  • lines changed 7, context: html, text, full: html, text
    4bb621ce7eb13b685bf5c9fde408220abda8d35e Wed Aug 24 12:08:48 2016 -0700
    Jonathan noticed in code review that I threw away some SO terms that appeared
    only in snp125Ui.c in e49078c1, and also suggested using a single mapping table
    instead of duplicating the mappings in soTerm.c. Better now. refs #17897, #17209
    Also corrected a SO term: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    4bb621ce7eb13b685bf5c9fde408220abda8d35e Wed Aug 24 12:08:48 2016 -0700
    Jonathan noticed in code review that I threw away some SO terms that appeared
    only in snp125Ui.c in e49078c1, and also suggested using a single mapping table
    instead of duplicating the mappings in soTerm.c. Better now. refs #17897, #17209
    Also corrected a SO term: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/estOrientInfo.c
  • lines changed 2, context: html, text, full: html, text
    370394fc362cce1b14f32e1a9d548fd5654063a0 Tue Aug 23 09:59:15 2016 -0700
    Account for bin column when loading estOrientInfo data.
    Add function to read selected PSLs from a table into memory.
    
• src/hg/lib/gpFx.c
  • lines changed 2, context: html, text, full: html, text
    4bb621ce7eb13b685bf5c9fde408220abda8d35e Wed Aug 24 12:08:48 2016 -0700
    Jonathan noticed in code review that I threw away some SO terms that appeared
    only in snp125Ui.c in e49078c1, and also suggested using a single mapping table
    instead of duplicating the mappings in soTerm.c. Better now. refs #17897, #17209
    Also corrected a SO term: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/gtexUi.c
  • lines changed 14, context: html, text, full: html, text
    5a63b70b7e8405a187c8fba71c557cca655e0424 Wed Aug 24 12:17:38 2016 -0700
    Add config option to display ENS geneId. For synergy with new GTEx gene sorter column. refs #17288
    
• src/hg/lib/pslReader.c
  • lines changed 13, context: html, text, full: html, text
    370394fc362cce1b14f32e1a9d548fd5654063a0 Tue Aug 23 09:59:15 2016 -0700
    Account for bin column when loading estOrientInfo data.
    Add function to read selected PSLs from a table into memory.
    
• src/hg/lib/soTerm.c
  • lines changed 68, context: html, text, full: html, text
    4bb621ce7eb13b685bf5c9fde408220abda8d35e Wed Aug 24 12:08:48 2016 -0700
    Jonathan noticed in code review that I threw away some SO terms that appeared
    only in snp125Ui.c in e49078c1, and also suggested using a single mapping table
    instead of duplicating the mappings in soTerm.c. Better now. refs #17897, #17209
    Also corrected a SO term: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    57d160dcebff420f967a4a740bfc2247510cccb3 Fri Aug 19 16:58:53 2016 -0700
    Oops, forgot to update the LRG date, thx Jonathan.
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 2, context: html, text, full: html, text
    57d160dcebff420f967a4a740bfc2247510cccb3 Fri Aug 19 16:58:53 2016 -0700
    Oops, forgot to update the LRG date, thx Jonathan.
    
• src/hg/makeDb/outside/gtexAnalysis/hub/gtexAnalysisHub.html
  • lines changed 12, context: html, text, full: html, text
    b47c3859109f101d73130bdaa4c1672d8170fac6 Thu Aug 25 10:12:52 2016 -0700
    Doc updates after QA review. refs #17885
    
  • lines changed 1, context: html, text, full: html, text
    69e9d519e0408cd6cb9cf58ac2493e2c93b732ad Thu Aug 25 13:26:34 2016 -0700
    Spelling fix. Thanks Chris. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/gtexAse.html
  • lines changed 5, context: html, text, full: html, text
    35c3ea759b6c694c8abade61042af14d462ce87d Thu Aug 25 09:19:11 2016 -0700
    Hack to allow QA before push to hgdownload. refs 17885
    
  • lines changed 20, context: html, text, full: html, text
    b47c3859109f101d73130bdaa4c1672d8170fac6 Thu Aug 25 10:12:52 2016 -0700
    Doc updates after QA review. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/hg19/trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    b47c3859109f101d73130bdaa4c1672d8170fac6 Thu Aug 25 10:12:52 2016 -0700
    Doc updates after QA review. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/hg38/trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    b47c3859109f101d73130bdaa4c1672d8170fac6 Thu Aug 25 10:12:52 2016 -0700
    Doc updates after QA review. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/hub.txt
  • lines changed 2, context: html, text, full: html, text
    4420faa925598081c2482af373656eda2deb28a8 Thu Aug 25 17:04:53 2016 -0700
    Fix hub description url. refs #17885
    
• src/hg/makeDb/trackDb/human/hg19/denisovaMethylation.html
  • lines changed 2, context: html, text, full: html, text
    f5a3afa84a9abf378a4ce2e35f85b085faa19938 Fri Aug 26 11:33:21 2016 -0700
    Correcting mistake in description of track coloring, refs #17958
    
• src/hg/makeDb/trackDb/human/hg19/neandertalMethylation.html
  • lines changed 2, context: html, text, full: html, text
    f5a3afa84a9abf378a4ce2e35f85b085faa19938 Fri Aug 26 11:33:21 2016 -0700
    Correcting mistake in description of track coloring, refs #17958
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    64469cd4922d5f83b772d6368ddabadd67619c22 Thu Aug 25 15:30:01 2016 -0700
    Removing priority level of snp146Common track as per code review, refs #17939
    
• src/hg/makeDb/trackDb/spUniprot.html
  • lines changed 1, context: html, text, full: html, text
    331e68951313b5a6219a877d80c21400ba53ab10 Wed Aug 24 10:01:48 2016 -0700
    Fixed a typo, refs #17717
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    b44348705e5f8e02de78440fc12e1fb8810864e3 Wed Aug 17 16:13:06 2016 -0700
    maybe dense is better for crispr track
    
• src/hg/near/hgNear/expRatio.c
  • lines changed 2, context: html, text, full: html, text
    c409aec3f90ff73e701681865ad4f4a0702bd4d1 Wed Aug 24 10:25:25 2016 -0700
    Friendlier configuration option for GTEx. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
  • lines changed 1, context: html, text, full: html, text
    f83f1af5fb9fe70b0002aa22820b913a1a3a6ef9 Mon Aug 22 12:31:25 2016 -0700
    Divide brain tissue section for easier viewing
    
  • lines changed 9, context: html, text, full: html, text
    50fc0b07eab1460b39d62c18a1906caf5f99f210 Wed Aug 24 13:55:37 2016 -0700
    Add column for GTEx Gene ID (ENS). To facilitate comparison with GTEx gene track. refs #17288
    
  • lines changed 1, context: html, text, full: html, text
    61562f06e83e4c4f24f759aed47342a499f5c736 Wed Aug 24 15:37:02 2016 -0700
    Lower GTEx max val to enhance signal in Gene Sorter. refs #17288
    
  • lines changed 1, context: html, text, full: html, text
    f2d118b97ee011247fdc735231bafcc05f1e44ef Wed Aug 24 16:09:24 2016 -0700
    Tuning GTEx distance and ratio tables for Gene Sorter. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/gtex.html
  • lines changed 58, context: html, text, full: html, text
    16c6acace66762d4716b2e8b58a1c0059034238c Wed Aug 24 10:16:41 2016 -0700
    Add doc for GTEx gene sorter column. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/gtexDistance.html
  • lines changed 11, context: html, text, full: html, text
    2c3c3eb4e95ac1e2ec067e8ade8b24bcdff946ce Thu Aug 25 11:53:37 2016 -0700
    Add doc for remaining GTEx Gene Sorter columns. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/gtexId.html
  • lines changed 4, context: html, text, full: html, text
    2c3c3eb4e95ac1e2ec067e8ade8b24bcdff946ce Thu Aug 25 11:53:37 2016 -0700
    Add doc for remaining GTEx Gene Sorter columns. refs #17288
    
• src/hg/near/makeNear.doc
  • lines changed 20, context: html, text, full: html, text
    bbde9065c89d41d21aa1df29d04b5892fc4af4e0 Wed Aug 24 10:24:57 2016 -0700
    Update table names in doc. refs #17288
    
  • lines changed 7, context: html, text, full: html, text
    f2d118b97ee011247fdc735231bafcc05f1e44ef Wed Aug 24 16:09:24 2016 -0700
    Tuning GTEx distance and ratio tables for Gene Sorter. refs #17288
    
  • lines changed 7, context: html, text, full: html, text
    8f85cfb621850ffe710909abca6d8d91cd1b8929 Thu Aug 25 13:02:46 2016 -0700
    Add hg38 tables to Gene Sorter. refs #17288
    
• src/hg/utils/genePredToProt/genePredToProt.c
  • lines changed 3, context: html, text, full: html, text
    326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700
    fixed case where exon becomes zero length
    
  • lines changed 74, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/combinedStopOptionsTest.prot.fa
  • lines changed 201, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/includeStopTest.prot.fa
  • lines changed 201, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa
  • lines changed 139, context: html, text, full: html, text
    326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700
    fixed case where exon becomes zero length
    
  • lines changed 12, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl
  • lines changed 1, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa
  • lines changed 49, context: html, text, full: html, text
    326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700
    fixed case where exon becomes zero length
    
  • lines changed 5, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa
  • lines changed 139, context: html, text, full: html, text
    326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700
    fixed case where exon becomes zero length
    
  • lines changed 12, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl
  • lines changed 1, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa
  • lines changed 49, context: html, text, full: html, text
    326c527afbeb869c709e48743e006ca276612c38 Sun Aug 21 15:46:27 2016 -0700
    fixed case where exon becomes zero length
    
  • lines changed 5, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/starForInframeStopsTest.prot.fa
  • lines changed 201, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/expected/translateSelnoTest.prot.fa
  • lines changed 201, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/genePredToProt/tests/input/refseq.grch38.gp
  • lines changed 3, context: html, text, full: html, text
    20becadd2c1dda0ccf5f5596be47a93e192e46ae Mon Aug 22 20:43:19 2016 -0700
    added options to genePredToProt to handle stop codons in various different ways
    
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 5, context: html, text, full: html, text
    52f36123f73c3f8858883650335673d15c2af787 Fri Aug 26 14:50:17 2016 -0700
    fixing clinvar broken outlinks, refs #17970
    
• src/product/installer/README.md
  • lines changed 2, context: html, text, full: html, text
    39446971199488a137bacc6c5eb6a02e0eda66ec Tue Aug 23 12:23:41 2016 -0700
    replacing .cse with .soe, refs #14399
    
• src/product/installer/browserSetup.sh
  • lines changed 4, context: html, text, full: html, text
    39446971199488a137bacc6c5eb6a02e0eda66ec Tue Aug 23 12:23:41 2016 -0700
    replacing .cse with .soe, refs #14399
    
• src/utils/newProg/newProg.c
  • lines changed 2, context: html, text, full: html, text
    7abe59581aad28213b586de54041c416cf1bf354 Mon Aug 22 11:07:43 2016 -0700
    Removing extra kentSrc line from generated makefile, refs #17687
    
• src/utils/qa/bigPush.sh
  • lines changed 14, context: html, text, full: html, text
    d0dfc899d227e86e3c5391019f1f2a1de296ca04 Thu Aug 25 14:53:24 2016 -0700
    Simplifying code that invokes verbose mode based on feedback from Chris in CR, refs #17728
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    d9ad3f41be0e03f7c856fb207dc5b663a2d10856 Mon Aug 29 10:04:55 2016 -0700
    v338 preview2 refs #17934
    

• lines changed: 1801
• files changed: 67