File Changes for angie

v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297

• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compiler warning for stricter format checkers (don't use variable in place of format argument).
• src/hg/hgSession/makefile
  • lines changed 2, context: html, text, full: html, text
    hgSession/makefile had an override of HG_WARN that prevented compilewarning from halting the build -- oops!
    
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/bedList.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/filterFields.c
  • lines changed 12, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/hgTables.c
  • lines changed 11, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/hgTables.h
  • lines changed 12, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/identifiers.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/intersect.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/joining.c
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTables/vcf.c
  • lines changed 67, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgTracks/variation.c
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo that caused hgTracks to ignore settings for coloringSNPs by exceptions. Thanks Brian L!
    fixes #12793
    
• src/hg/hgTracks/vcfTrack.c
  • lines changed 95, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 12, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgVai/libifyMe.c
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/hgc/vcfClick.c
  • lines changed 59, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 1, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/inc/customPp.h
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 17, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/customFactory.c
  • lines changed 155, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 4, context: html, text, full: html, text
    Handle blank line(s) preceding header lines that specify format.
• src/hg/lib/customPp.c
  • lines changed 16, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/lib/pgSnp.c
  • lines changed 9, context: html, text, full: html, text
    Added a few tests for 0-length (insertion) variants, to avoid errAbortwhen trying to fetch sequence for empty region.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 28, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 82, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/tests/input/annoGrator/indelTrim.vcf
  • lines changed 17, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/hg/lib/vcfUi.c
  • lines changed 15, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
• src/inc/vcf.h
  • lines changed 5, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 9, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/lib/annoStreamVcf.c
  • lines changed 1, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 1, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.
    
• src/lib/bamFile.c
  • lines changed 3, context: html, text, full: html, text
    Fixing an incomplete renaming of a variable that caused a compile errorfor a mirror admin using USE_BAM w/samtools but not using KNETFILE_HOOKS.
    refs #12827
    
• src/lib/vcf.c
  • lines changed 65, context: html, text, full: html, text
    Adding support for plain VCF custom tracks (as opposed to VCF+tabix),since users seem to want to upload VCF, and as long as the file is
    not too big it will work OK. This means adding a new track type
    vcf (as opposed to vcfTabix) and supporting it in hgTracks, hgTrackUi,
    hgc, hgTables and hgVai. (and others I've forgotten?)
    refs #12416
    
  • lines changed 114, context: html, text, full: html, text
    In addition to trimming the left padding base from VCF indels,now we trim identical bases on the right of all alleles, if there
    are any. I've seen multiple cases of user VCF with indels that
    have inflated size due to including right flanking bases; when
    trying to determine functional consequences, it's misleading to
    have an indel sized larger than it has to be.