All File Changes

v337_base to v338_preview (2016-08-15 to 2016-08-22) v338

• confs/hgwbeta.hg.conf
  • lines changed 6, context: html, text, full: html, text
    8d31d22f330f6b1f258a79b385079a70b7f77854 Sun Aug 21 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/aladdin/aladdin/aladdin.c
  • lines changed 3, context: html, text, full: html, text
    90339aa1d74677c8180a416e9361280acfab9caa Tue Aug 16 19:23:22 2016 -0700
    fix compilation error with C99 style inline used by default by clang on OS/X
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 4, context: html, text, full: html, text
    90840eea84ff22cf479d884b286de941abfe9f81 Mon Aug 15 14:05:12 2016 -0700
    making gbib default to non-https, refs #17906
    
• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 4, context: html, text, full: html, text
    b3fcbb7d6139a1993f5f02261ae3b495bc3edf41 Mon Aug 15 10:43:26 2016 -0700
    Increased verbosity level to 2 for no match & no table info lines.
    
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 13, context: html, text, full: html, text
    53280f702308da193ac7565e25d29d571e06d3b7 Fri Aug 19 10:51:59 2016 -0700
    Added a check for bad chrom name for scaffold-based assemblies. All other checks are still skipped for scaffold-based assemblies! refs #17919
    
• src/hg/cirm/cdw/cdwCleanMetaData/cdwCleanMetaData
  • lines changed 122, context: html, text, full: html, text
    17ecc359976eaed89a1380b3b159a6a7f6b785ff Wed Aug 17 13:14:06 2016 -0700
    A script that cleans up meta data files, refs #17918
    
  • lines changed 6, context: html, text, full: html, text
    87fe7735b35667d812e378fa2e307231b3913328 Fri Aug 19 11:12:46 2016 -0700
    Fixing a small bug and making it a bit faster. refs #17918
    
• src/hg/cirm/cdw/cdwCleanMetaData/makefile
  • lines changed 6, context: html, text, full: html, text
    17ecc359976eaed89a1380b3b159a6a7f6b785ff Wed Aug 17 13:14:06 2016 -0700
    A script that cleans up meta data files, refs #17918
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 13, context: html, text, full: html, text
    8235f06135567f93c0e03815c2c19908b454c997 Mon Aug 15 10:35:20 2016 -0700
    Make it automatically create cdwDownloadToken table if it doesn't exist.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 4, context: html, text, full: html, text
    5c8135640b78a11f5d50f945e6ef9aab0e1d758e Mon Aug 15 10:16:15 2016 -0700
    Adding code generated files to go with new cdw.as.
    
  • lines changed 4, context: html, text, full: html, text
    277b84f3aff3d059cf56dd82d8f371012f6cc738 Wed Aug 17 13:17:37 2016 -0700
    adding in the wrangler column to the databases
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 17, context: html, text, full: html, text
    5c8135640b78a11f5d50f945e6ef9aab0e1d758e Mon Aug 15 10:16:15 2016 -0700
    Adding code generated files to go with new cdw.as.
    
  • lines changed 17, context: html, text, full: html, text
    277b84f3aff3d059cf56dd82d8f371012f6cc738 Wed Aug 17 13:17:37 2016 -0700
    adding in the wrangler column to the databases
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 274, context: html, text, full: html, text
    5c8135640b78a11f5d50f945e6ef9aab0e1d758e Mon Aug 15 10:16:15 2016 -0700
    Adding code generated files to go with new cdw.as.
    
  • lines changed 274, context: html, text, full: html, text
    277b84f3aff3d059cf56dd82d8f371012f6cc738 Wed Aug 17 13:17:37 2016 -0700
    adding in the wrangler column to the databases
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 1, context: html, text, full: html, text
    375825e47ff35dc526e756a40b582f143f853219 Mon Aug 15 10:14:18 2016 -0700
    Making sequencer controlled vocab for generic Illumina match tag spread scheet exactly.
    
• src/hg/cirm/cdw/utils/cdwFastqPolyFilter/cdwFastqPolyFilter.c
  • lines changed 1, context: html, text, full: html, text
    ddbce2e40065419dd313f6870e11a66993180628 Mon Aug 15 10:13:30 2016 -0700
    Improving a comment.
    
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/getRnaPred/getRnaPred.c
  • lines changed 9, context: html, text, full: html, text
    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra
  • lines changed 4, context: html, text, full: html, text
    0cd760e9b401d1b044f1b2bb47707be351a3a11c Thu Aug 18 15:35:36 2016 -0700
    Providing otherOrgs links to RGD for rat on hgGene pages, refs #14480
    
• src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
  • lines changed 3, context: html, text, full: html, text
    0cd760e9b401d1b044f1b2bb47707be351a3a11c Thu Aug 18 15:35:36 2016 -0700
    Providing otherOrgs links to RGD for rat on hgGene pages, refs #14480
    
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/hgTables/identifiers.c
  • lines changed 6, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 5, context: html, text, full: html, text
    d371431b09ee29373cf24d57f387f8dd0bee4ab9 Wed Aug 17 17:10:30 2016 -0700
    changed to compile on OS/X
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 5, context: html, text, full: html, text
    ed0199b6ca7d6cc30154cdb537adae9850732f4f Wed Aug 10 15:21:41 2016 -0700
    Add cart var to suppress whiteout behind GTEX graph. Use this so highlighting will extend through GTEx items.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    38990114981b7e195d33206edd471797038c6557 Thu Aug 18 11:16:36 2016 -0700
    Fixing XSS. Changed output from just printf to warn() which gets properly encoded output.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 8, context: html, text, full: html, text
    bc258de35963243ad39adc04b4500a21354cd20b Tue Aug 16 13:13:54 2016 -0700
    Minor changes to PSL protein query section, refs #17662
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    dc41d775e7d4176838627ca728cba7429df46ce0 Wed Aug 17 08:32:12 2016 -0700
    made a correction per code review #17904
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    8b0b16234cb0fbda83270567032e5b35b1e9fced Mon Aug 15 14:03:21 2016 -0700
    fixed tag for malayan flying lemur announcement
    
  • lines changed 1, context: html, text, full: html, text
    e022572c9f1c2c4827628af5adf25dd96c0f9ea1 Mon Aug 15 14:06:21 2016 -0700
    corrected typo, again
    
  • lines changed 46, context: html, text, full: html, text
    53997a88c2155abf13872ebb04605968afc54bc8 Tue Aug 16 14:45:25 2016 -0700
    Announcing snp147 tracks, refs #17209
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 3, context: html, text, full: html, text
    0a1bc7084b646e57a819ab7fbec1222cc2151f51 Fri Aug 19 13:29:30 2016 -0700
    Updating date and PMCID on pubs.html page
    
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    53997a88c2155abf13872ebb04605968afc54bc8 Tue Aug 16 14:45:25 2016 -0700
    Announcing snp147 tracks, refs #17209
    
• src/hg/inc/gtexAse.h
  • lines changed 89, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 9, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
  • lines changed 1, context: html, text, full: html, text
    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/inc/gtexTissue.h
  • lines changed 3, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/inc/gtexUi.h
  • lines changed 4, context: html, text, full: html, text
    ed0199b6ca7d6cc30154cdb537adae9850732f4f Wed Aug 10 15:21:41 2016 -0700
    Add cart var to suppress whiteout behind GTEX graph. Use this so highlighting will extend through GTEx items.
    
• src/hg/inc/hgHgvs.h
  • lines changed 74, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    1fd0a93c6c416ff64656ef6b2e0a3a640153ec2e Wed Aug 17 11:45:11 2016 -0700
    changes after code review: moved whitespace before star, added a whitespace after for, removed debug statement, refs #17859
    
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    d26a087dff59f4e4493e4ce2cf7d5b1ae145fdf3 Thu Aug 18 12:15:52 2016 -0700
    adding back commits reverted earlier that got lost in the final merge. XSS fixes.
    
• src/hg/lib/cartJson.c
  • lines changed 1, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/lib/genbank.c
  • lines changed 1, context: html, text, full: html, text
    d371431b09ee29373cf24d57f387f8dd0bee4ab9 Wed Aug 17 17:10:30 2016 -0700
    changed to compile on OS/X
    
• src/hg/lib/gtexAse.as
  • lines changed 16, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 8, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
  • lines changed 1, context: html, text, full: html, text
    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/lib/gtexAse.c
  • lines changed 214, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 43, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/lib/gtexAse.sql
  • lines changed 22, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 8, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
  • lines changed 1, context: html, text, full: html, text
    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/lib/gtexTissue.as
  • lines changed 1, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/lib/gtexTissue.c
  • lines changed 19, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/lib/gtexTissue.sql
  • lines changed 1, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    d26a087dff59f4e4493e4ce2cf7d5b1ae145fdf3 Thu Aug 18 12:15:52 2016 -0700
    adding back commits reverted earlier that got lost in the final merge. XSS fixes.
    
  • lines changed 60, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/hgHgvs.c
  • lines changed 531, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/hui.c
  • lines changed 0, context: html, text, full: html, text
    1fd0a93c6c416ff64656ef6b2e0a3a640153ec2e Wed Aug 17 11:45:11 2016 -0700
    changes after code review: moved whitespace before star, added a whitespace after for, removed debug statement, refs #17859
    
  • lines changed 5, context: html, text, full: html, text
    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 1, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 11, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/hgvsTester.c
  • lines changed 72, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/hgvsTests.mk
  • lines changed 18, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/input/hgvs/validTerms.txt
  • lines changed 16, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/lib/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 71, context: html, text, full: html, text
    2f00917f91bad02970b7e8700560203f6393bbf9 Tue Aug 16 11:47:06 2016 -0700
    Docs for bosTau8 snp148, refs #16846
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 71, context: html, text, full: html, text
    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
  • lines changed 13, context: html, text, full: html, text
    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 2, context: html, text, full: html, text
    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 32, context: html, text, full: html, text
    0cd760e9b401d1b044f1b2bb47707be351a3a11c Thu Aug 18 15:35:36 2016 -0700
    Providing otherOrgs links to RGD for rat on hgGene pages, refs #14480
    
• src/hg/makeDb/outside/gtexAnalysis/README.txt
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    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/makeDb/outside/gtexAnalysis/buildNotes.ase.txt
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    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
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    6a99e0e1adc5f0e60092d58ae73cb40bbfd20463 Wed Aug 10 13:10:03 2016 -0700
    Remove initial experiment work. Add new summary graph (just starting)
    
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/filelist.txt
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/genomes.txt
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
    Finish up ASE tracks. Polish hub for release. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/gtexAnalysisHub.html
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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• src/hg/makeDb/outside/gtexAnalysis/hub/gtexAse.html
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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    7abd8e0cb2d83c0e1f345d6635e8c5b44a233d9c Thu Aug 18 16:45:27 2016 -0700
    Response to QA review. refs #17885
    
• src/hg/makeDb/outside/gtexAnalysis/hub/hg19/trackDb.txt
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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    7abd8e0cb2d83c0e1f345d6635e8c5b44a233d9c Thu Aug 18 16:45:27 2016 -0700
    Response to QA review. refs #17885
    
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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    7abd8e0cb2d83c0e1f345d6635e8c5b44a233d9c Thu Aug 18 16:45:27 2016 -0700
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• src/hg/makeDb/outside/gtexAnalysis/hub/hub.test.txt
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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• src/hg/makeDb/outside/gtexAnalysis/hub/hub.txt
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    9e2a8a0b99b50e87a71b0bf1f9f6df74f06c708e Mon Aug 15 12:48:20 2016 -0700
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• src/hg/makeDb/outside/hgGtexAse/hgGtexAse.c
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    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
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    013ccd312d93bfb526241f9d81c4327a3b169b2e Tue Aug 9 14:52:59 2016 -0700
    Extend gtexAse file format to include quartiles, donors. Add GTEx abbreviation to tissue table. Generalize the new hub as GTex analysis.
    
• src/hg/makeDb/outside/hgGtexAse/makefile
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    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
• src/hg/makeDb/outside/makefile
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    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
• src/hg/makeDb/schema/all.joiner
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    7f1d92b173ea8fe0d8045dbb3f0d0906d9a638b5 Mon Aug 15 13:03:17 2016 -0700
    remove braNey* assemblies from all.joiner
    
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    fc6310e34ccd5e9af939f5c83d7ff3f833fde3c7 Thu Aug 18 15:58:58 2016 -0700
    Adding rn6.ensToRgd to joiner file, refs #14480
    
• src/hg/makeDb/trackDb/galVar/galVar1/description.html
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    918cc2bf0c55c14333dcd964587f31ea6eb336da Wed Aug 17 08:36:53 2016 -0700
    made a few corrections per code review #17904
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
• src/hg/makeDb/trackDb/human/trackDb.gtexAwgAse.ra
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    ba22bbbe65670b6378e16e7d60a214102e600a8f Thu Jun 30 19:10:06 2016 -0700
    Initial load of GTEx ASE data from NY Genome Center (Analysis group lab)
    
• src/hg/makeDb/trackDb/human/trackDb.ra
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    6c0629f88df5fdcdce822840721d739c774a5b3b Tue Aug 16 13:20:12 2016 -0700
    Hiding snp146Common track by default for release of new snp147 track, refs #17209
    
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
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    21b9d6eee8b8cb0380c3349caa8af0fa90cd9174 Wed Aug 17 11:04:37 2016 -0700
    adding note about galGal5 parameters refs #17168
    
• src/hg/makeDb/trackDb/trackDb.ra
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    ae65086ea86753e1cd15237d3cf2d908231d7bb2 Wed Aug 17 14:12:08 2016 -0700
    label change of crispr track
    
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    32363149512bedac39605a826afa3e565357e4b6 Wed Aug 17 16:09:28 2016 -0700
    fixing crispr trackDb again
    
• src/hg/near/hgExpDistance/hgMaxExp.c
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    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
• src/hg/near/hgExpDistance/makefile
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    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/columnDb.ra
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    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
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    d6d046f86ee0386264a3bd359a2f0d2cc0d05434 Thu Aug 18 17:22:28 2016 -0700
    Configuration ready for CGI push. Still needs doc files. SHould be fine w/o tables. refs #17288
    
• src/hg/near/hgNear/hgNearData/Human/orderDb.ra
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    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
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    d6d046f86ee0386264a3bd359a2f0d2cc0d05434 Thu Aug 18 17:22:28 2016 -0700
    Configuration ready for CGI push. Still needs doc files. SHould be fine w/o tables. refs #17288
    
• src/hg/near/makeNear.doc
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    f38078ce59f74d48998cad7e5cfe810fa5c4c08a Thu Aug 18 17:16:19 2016 -0700
    Add GTEx to gene sorter. refs #17288
    
• src/hg/utils/automation/asmHubSimpleRepeat.pl
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    dc8e0543646e48a1b8cb08c34a7b6c77c25bf9cf Thu Aug 18 10:13:33 2016 -0700
    adding augustus gene to trackDb and fixup errors refs #13553
    
• src/hg/utils/automation/asmHubTrackDb.sh
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    dc8e0543646e48a1b8cb08c34a7b6c77c25bf9cf Thu Aug 18 10:13:33 2016 -0700
    adding augustus gene to trackDb and fixup errors refs #13553
    
• src/hg/utils/automation/asmHubWindowMasker.pl
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    dc8e0543646e48a1b8cb08c34a7b6c77c25bf9cf Thu Aug 18 10:13:33 2016 -0700
    adding augustus gene to trackDb and fixup errors refs #13553
    
• src/hg/utils/automation/doAssemblyHub.pl
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    b6ce4b94768fc2c6587b94268d82a94842141181 Thu Aug 18 09:31:36 2016 -0700
    adding augustus gene track construction and clean up references to work hubs refs #13553
    
• src/hg/utils/automation/doAugustus.pl
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    b6ce4b94768fc2c6587b94268d82a94842141181 Thu Aug 18 09:31:36 2016 -0700
    adding augustus gene track construction and clean up references to work hubs refs #13553
    
• src/hg/utils/automation/doEnsGeneUpdate.pl
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    2387766791f74cfaf8485356ea076687c7131e98 Mon Aug 15 11:34:47 2016 -0700
    do not remove the dot version from the gene name when verifying correspondence with pepTide name they all have version numbers now refs #17863
    
• src/hg/utils/automation/doNcbiRefSeq.pl
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    f8c07173c3cc28fd490f767f24c511bca329bd89 Fri Aug 19 16:09:00 2016 -0700
    clean up and annotate generated processing shell files refs #13673
    
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    b69912c01829ac1b162eac9c43f801a049b07778 Fri Aug 19 18:14:17 2016 -0700
    eliminate bad records to allow continue refs #13673
    
• src/hg/utils/automation/gff3ToRefLink.pl
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    b69912c01829ac1b162eac9c43f801a049b07778 Fri Aug 19 18:14:17 2016 -0700
    eliminate bad records to allow continue refs #13673
    
• src/hg/utils/genePredToProt/genePredToProt.c
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
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    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
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    3a90d3637f25ea59ea95bcbae8cf0dd63ff4fbfd Sun Aug 21 15:11:50 2016 -0700
    fixed bug where CDS is empty when last condon is incomplete
    
• src/hg/utils/genePredToProt/makefile
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
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    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
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    6fa9908b5a36a45fb2f951157395de0a9a953a17 Sat Aug 20 09:14:32 2016 -0700
    removed duplicate targets in makefile
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.fa
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    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
    to the protin and cds ids.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.cds.psl
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    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
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• src/hg/utils/genePredToProt/tests/expected/refSeqSuffixTest.prot.fa
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    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
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• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.fa
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/genePredToProt/tests/expected/refSeqTest.cds.psl
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    2b39df1c5734d12c598ee15f6fe27ecb5798ef68 Sun Aug 21 09:15:11 2016 -0700
    Added option to output PSL of CDS alignment and to add suffixes
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• src/hg/utils/genePredToProt/tests/expected/refSeqTest.prot.fa
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/genePredToProt/tests/input/refseq.grch38.gp
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    fc5b9650f28c87f2757a97a44c0c1682538725c0 Fri Aug 19 17:42:53 2016 -0700
    fixed incorrect help message
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
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    15792863307e32e65004b2db403c305c4fdd2532 Thu Aug 18 15:45:49 2016 -0700
    adding dropQ and dropT arguments to avoid garbage in NCBI gff3 files refs #13673
    
• src/hg/utils/makefile
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    7edc888861d9fd7769d0a21ae55d5f3e75e61587 Fri Aug 19 17:06:17 2016 -0700
    Added genePredToProt that translates genePred files to protein.
    It handles cases where there the annotations has frameshifting
    indels described in the exonFrames column. Partial codons will be skipped.
    This differs from getRnaPred, which only handles initial, incomplete codons.
    
• src/inc/dnautil.h
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    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/inc/htmshell.h
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    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
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    d26a087dff59f4e4493e4ce2cf7d5b1ae145fdf3 Thu Aug 18 12:15:52 2016 -0700
    adding back commits reverted earlier that got lost in the final merge. XSS fixes.
    
• src/inc/regexHelper.h
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    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/inc/twoBit.h
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    017f1ebbfad81dd9a4759d391debdc44b227b595 Fri Aug 19 23:25:17 2016 -0700
    Cache twoBit sequence header information for the last sequence
    accessed to avoid rereading N and mask blocks when sequentially
    reader fragments of the genome. This resulted in a 20% speedup
    for pslRecalcMatch.
    
• src/lib/dnautil.c
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    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/lib/htmshell.c
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    2817400f77ca691cedbc23df32154f00c0a4a77f Wed Aug 17 22:14:46 2016 -0700
    This commit refs #17815, #17782. Addressing XSS issues in warn and errAbort via new htmlSafef and encoding for several cases including html, attribrute, css, js, url or none. Encoding approach is based on OWASP recommendations.
    
• src/lib/regexHelper.c
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    aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
    Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
    and protein (p.) simple substitutions relative to NP_.
    Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
    hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
    out-of-bounds coordinates and mismatching reference alleles.
    refs #15071, #15554
    
• src/lib/twoBit.c
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    017f1ebbfad81dd9a4759d391debdc44b227b595 Fri Aug 19 23:25:17 2016 -0700
    Cache twoBit sequence header information for the last sequence
    accessed to avoid rereading N and mask blocks when sequentially
    reader fragments of the genome. This resulted in a 20% speedup
    for pslRecalcMatch.
    
• src/product/installer/browserSetup.sh
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    2260826b39f20399369f420685290b4d0e59922b Mon Aug 15 15:21:18 2016 -0700
    changing gbic script so it does not default to https
    
• src/utils/qa/weeklybld/buildEnv.csh
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    1834d84f11c73a2ad3a3429c02941a5a3c6439b0 Mon Aug 22 10:05:41 2016 -0700
    v338 preview1 refs #17833
    

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