File Changes for angie

v249_preview2 to v249_base (2011-03-22 to 2011-03-29) v249

• src/hg/hgTables/gffOut.c
  • lines changed 22, context: html, text, full: html, text
    Bug #2964 (Table Browser: RefGene output in GTF gives error):An unanticipated condition led to an errAbort: rn4 refGene contained a transcript (alternate alignment of NM_001008876) with the coding region annotated as the first base of the first exon. Now, instead of errAborting when a requested codon offset is out of bounds, we don't attempt to print start_codon or stop_codon elements when the entire codon is not contained in the transcript's exons and coding region.
• src/hg/hgTracks/bamTrack.c
  • lines changed 29, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/hgTracks.c
  • lines changed 17, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/hgTracks.h
  • lines changed 15, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 54, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 429, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/vcfClick.c
  • lines changed 244, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/lib/customFactory.c
  • lines changed 60, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 24, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132Common.html
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132NonUnique.html
  • lines changed 7, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132Patient.html
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/inc/linefile.h
  • lines changed 2, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
• src/inc/vcf.h
  • lines changed 1, context: html, text, full: html, text
    Fixing copy-paste misnomer found by Mark.
  • lines changed 50, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/linefile.c
  • lines changed 5, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
  • lines changed 2, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/expected/vcfParse1kGNoGenotypes.out
  • lines changed 1, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
• src/lib/tests/expected/vcfParse1kGWithGenotypes.out
  • lines changed 1, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
• src/lib/tests/expected/vcfParseOldV3.out
  • lines changed 44, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/input/20091110_pilot1_vcf_merged_call_sets_YRI.2and3_way.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/input/20091110_pilot1_vcf_merged_call_sets_YRI.2and3_way.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/tabixFetch.c
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
• src/lib/tests/vcfParseTest.c
  • lines changed 4, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
  • lines changed 2, context: html, text, full: html, text
    Replacing atoi with sqlUnsigned as suggested by Mark.
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
  • lines changed 103, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.