File Changes for angie

v258_base to v259_preview (2011-10-10 to 2011-10-25) v259

• src/hg/hgTables/joining.c
  • lines changed 60, context: html, text, full: html, text
    Bug #5591 (dup. GO id's in joining query w/knownGene, kgXref):1. Band-aid: remove successive duplicates from joined output. It would be better to prevent duplicate queries upstream, but significantly more work. 2. Got rid of unnecessary duplication of code (joinedTablesTabOut and joinedTablesTabOutFile) that would have required the same fix in two places.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    Registered track handlers for snp135 tables, to make sure they're in the next release.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 102, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added filtering on minor allelefrequency (actually, 1 - major allele frequency), if INFO column contains the AF tag, or AC and AN tags. Also, in vcfTrack.c, fixed a bug in multi-allele abbreviation code in vcfFileToPgSnp.
  • lines changed 39, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/hgc/vcfClick.c
  • lines changed 2, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/inc/vcfUi.h
  • lines changed 3, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added filtering on minor allelefrequency (actually, 1 - major allele frequency), if INFO column contains the AF tag, or AC and AN tags. Also, in vcfTrack.c, fixed a bug in multi-allele abbreviation code in vcfFileToPgSnp.
  • lines changed 2, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/lib/cart.c
  • lines changed 21, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    Fixing stricter compiler warning (warning: format not a string literal and no format arguments)
• src/hg/lib/vcfUi.c
  • lines changed 16, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added filtering on minor allelefrequency (actually, 1 - major allele frequency), if INFO column contains the AF tag, or AC and AN tags. Also, in vcfTrack.c, fixed a bug in multi-allele abbreviation code in vcfFileToPgSnp.
  • lines changed 19, context: html, text, full: html, text
    Code review advice from Tim about how to properly use ClosestToHome.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 43, context: html, text, full: html, text
    Track #34 (dbVar / ISCA): Removed "Retrospective" from the track namesbecause prospective data are included now. Reloaded both hg18 and hg19 isca* with both "submitted" (on this assembly) and "remapped" (from some other assembly) files from dbVar. Changed subtrack order to match ISCA custom tracks' order.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 74, context: html, text, full: html, text
    Track #34 (dbVar / ISCA): Added iscaRetrospective subtracks to hg19,including two new subtracks (likely benign & likely pathogenic) for categories that were not present when I loaded data into hg18.
  • lines changed 28, context: html, text, full: html, text
    Track #34 (dbVar / ISCA): Removed "Retrospective" from the track namesbecause prospective data are included now. Reloaded both hg18 and hg19 isca* with both "submitted" (on this assembly) and "remapped" (from some other assembly) files from dbVar. Changed subtrack order to match ISCA custom tracks' order.
  • lines changed 66, context: html, text, full: html, text
    Track #1702 (DGV update): Loaded DGV's beta data in new file format into hg19.This is just a dry run to check out the new format, no need to QA until their data integration is complete.
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 123, context: html, text, full: html, text
    Track #34 (dbVar/ISCA): forgot to rename .html when renaming tracks, thanks b0b for catching!
• src/hg/makeDb/trackDb/human/iscaRetrospectiveComposite.html
  • lines changed 123, context: html, text, full: html, text
    Track #34 (dbVar/ISCA): forgot to rename .html when renaming tracks, thanks b0b for catching!
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 29, context: html, text, full: html, text
    Track #34 (dbVar / ISCA): Added iscaRetrospective subtracks to hg19,including two new subtracks (likely benign & likely pathogenic) for categories that were not present when I loaded data into hg18.
  • lines changed 56, context: html, text, full: html, text
    Track #34 (dbVar / ISCA): Removed "Retrospective" from the track namesbecause prospective data are included now. Reloaded both hg18 and hg19 isca* with both "submitted" (on this assembly) and "remapped" (from some other assembly) files from dbVar. Changed subtrack order to match ISCA custom tracks' order.
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    Removing unwanted double-quote at end of line that is pulled in by loosened regex.