File Changes for angie

v290_preview2 to v290_base (2013-09-23 to 2013-09-30) v290

• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/annoGratorGpVar.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/gpFx.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/soTerm.h
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/inc/variant.h
  • lines changed 6, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/annoFormatVep.c
  • lines changed 47, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 54, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/gpFx.c
  • lines changed 633, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/soTerm.c
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 1, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/hg/lib/variant.c
  • lines changed 8, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771
    
• src/lib/annoStreamVcf.c
  • lines changed 4, context: html, text, full: html, text
    Code review feedback, thanks Tim.refs #11800
    
• src/lib/vcf.c
  • lines changed 2, context: html, text, full: html, text
    Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
    exons and building a new genePred along with a sequence that has
    one exon's modification, we project the variant start and end onto
    cDNA and CDS coords up front. Then there is only one modification
    to make per allele, and in fact we only care about the actual
    modification when there's a CDS change.
    A new SO term, exon_loss, has been incorporated into gpFx and
    hgVai's/annoGratorGpVar's filtering.
    fixes #11771