File Changes for angie

v337_preview2 to v337_base (2016-08-08 to 2016-08-15) v337

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    8e0a4db9b5cf81ab6826ea086a6aca749934e5e9 Mon Aug 8 14:17:43 2016 -0700
    Fixing typo caught by Christopher Lee. refs #17209 note-53
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
    Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
    
• src/hg/inc/soTerm.h
  • lines changed 3, context: html, text, full: html, text
    e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
    Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
    
• src/hg/lib/hdb.c
  • lines changed 26, context: html, text, full: html, text
    d185918b081b11e5e66133f6d147cf6220b54f81 Fri Aug 12 14:52:31 2016 -0700
    Make hDbForTaxon more discerning about extra fluff in defaultDb and dbDb: order multiple matches in defaultDb by dbDb.orderKey, require active=1 and check database existence. refs #17886
    
• src/hg/lib/snp125Ui.c
  • lines changed 58, context: html, text, full: html, text
    e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
    Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
    
• src/hg/lib/soTerm.c
  • lines changed 55, context: html, text, full: html, text
    e49078c13bb3c9243511050a99f54455db3aa1b8 Fri Aug 12 16:24:48 2016 -0700
    Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c. soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee). Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now. refs #17209
    
• src/hg/makeDb/doc/hg18.txt
  • lines changed 13, context: html, text, full: html, text
    955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
    DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 24, context: html, text, full: html, text
    955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
    DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
    
  • lines changed 23, context: html, text, full: html, text
    aad8186bd6883ae5debe29a690e36176d1a9e9a9 Thu Aug 11 10:20:51 2016 -0700
    LRG tracks updated for hg19 and hg38. refs #13359
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 20, context: html, text, full: html, text
    aad8186bd6883ae5debe29a690e36176d1a9e9a9 Thu Aug 11 10:20:51 2016 -0700
    LRG tracks updated for hg19 and hg38. refs #13359
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 24, context: html, text, full: html, text
    955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
    DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    55ab91a9a8d5ed3b43d794b03085eaa93b120910 Fri Aug 12 15:12:03 2016 -0700
    Correcting copy-pasted settings for linking to orthologous positions in chimp and macaque from SNPs tracks. HT Christopher Lee. refs #17209
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    955e94313201c638db291235ee6198f7d59e080c Wed Aug 10 10:51:22 2016 -0700
    DGV 2016 update. trackDb.ra has alpha and beta,public stanzas with different dataVersion. refs #17351
    
  • lines changed 40, context: html, text, full: html, text
    55ab91a9a8d5ed3b43d794b03085eaa93b120910 Fri Aug 12 15:12:03 2016 -0700
    Correcting copy-pasted settings for linking to orthologous positions in chimp and macaque from SNPs tracks. HT Christopher Lee. refs #17209
    
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    1c97569bf82e2552afd965837460817e10b5dff2 Fri Aug 12 15:10:25 2016 -0700
    Removing human-specific snp track settings from mouse/trackDb.ra.