File Changes for angie

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 63, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    Track #8360 (snp137): registering track handlers (late!).
• src/hg/hgTracks/variation.c
  • lines changed 10, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/hgc/hgc.c
  • lines changed 72, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 241, context: html, text, full: html, text
    Doc #5088 (clean up trackDb/README): added documentation for variationtrack settings, including moving snpNNN into a new type. Technically
    it is still bed 6 +, but I plan to make it a proper type so I can stop
    hardcoding registerTrackHandler's. Also removed some hardcoded hostnames
    in doc HREF's.
    
  • lines changed 1, context: html, text, full: html, text
    Typo fix for previous commit (#5088)
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 220, context: html, text, full: html, text
    Doc #5088 (clean up trackDb/README): added documentation for variationtrack settings, including moving snpNNN into a new type. Technically
    it is still bed 6 +, but I plan to make it a proper type so I can stop
    hardcoding registerTrackHandler's. Also removed some hardcoded hostnames
    in doc HREF's.
    
• src/hg/inc/snp125CodingCoordless.h
  • lines changed 1, context: html, text, full: html, text
    Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
    also had NULL frame... although that may be a red flag for the cds-indel's.
    I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
    
• src/hg/inc/snp125Ui.h
  • lines changed 5, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/lib/snp125Coding.sql
  • lines changed 1, context: html, text, full: html, text
    Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
    also had NULL frame... although that may be a red flag for the cds-indel's.
    I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
    
• src/hg/lib/snp125CodingCoordless.c
  • lines changed 1, context: html, text, full: html, text
    Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
    also had NULL frame... although that may be a red flag for the cds-indel's.
    I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
    
• src/hg/lib/snp125CodingCoordless.sql
  • lines changed 1, context: html, text, full: html, text
    Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
    also had NULL frame... although that may be a red flag for the cds-indel's.
    I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
    
• src/hg/lib/snp125Ui.c
  • lines changed 91, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    Track #8360 (snp137): regenerated snp137CodingDbSnp after finding that itwas omitting func code 43 (stop-loss) and many rows with 45 (cds-indel) that
    also had NULL frame... although that may be a red flag for the cds-indel's.
    I am waiting to hear back from dbSNP about some possible misuses of cds-indel.
    
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    Fixing typo that broke compile.
• src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
  • lines changed 110, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):at Ensembl's request, instead of displaying dbSNP's predicted function terms, instead show
    terms from the Sequence Ontology (SO). Where possible, terms from Ensembl's list at
    http://staging.ensembl.org/info/docs/variation/predicted_data.html are used.
    
• src/hg/near/hgNear/hgNear.c
  • lines changed 4, context: html, text, full: html, text
    Fixing stricter-gcc compiler warning 'format not a string literal and no format arguments' (cartWebStart needs a proper format string).