File Changes for angie

v361_base to v362_preview (2018-02-12 to 2018-02-19) v362

• src/hg/inc/variantProjector.h
  • lines changed 7, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
  • lines changed 2, context: html, text, full: html, text
    849d61bdaf65ea095a541f848e5af89edd85bf4a Fri Feb 16 16:06:56 2018 -0800
    Fixing outdated comment
• src/hg/lib/annoGratorGpVar.c
  • lines changed 11, context: html, text, full: html, text
    0d21bf4a4674bf1e93e4db5cf51ba3053e7c7770 Thu Feb 15 13:17:13 2018 -0800
    Thanks ChrisL for noticing that HGVS g. terms were missing for intergenic variants. refs #20981
  • lines changed 2, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/lib/variantProjector.c
  • lines changed 59, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
  • lines changed 2, context: html, text, full: html, text
    849d61bdaf65ea095a541f848e5af89edd85bf4a Fri Feb 16 16:06:56 2018 -0800
    Fixing outdated comment
• src/hg/makeDb/schema/all.joiner
  • lines changed 14, context: html, text, full: html, text
    c21933750b24b2bec860e88050b5119d28f63a62 Mon Feb 12 15:36:35 2018 -0800
    Apply ncbiRefSeq rules to any genome database that has ncbiRefSeq tables (hopefully one day they all will, or most at least).
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_agree.vcf
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf
  • lines changed 4, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
  • lines changed 1, context: html, text, full: html, text
    babee48a4214661f14263cc1ac8bc93605001b73 Fri Feb 16 15:44:53 2018 -0800
    Added function vpExpandIndelGaps, which examples a PSL's gaps to see if any of them are ambiguously placed indels between genome and transcript. If so, it expands them into double-sided gaps so that vpGenomicToTranscript doesn't miss those g-t indels due to arbitrary placement of gaps. As a side-effect, when a change to the genome means no change to the transcript, vp may assert a larger range of no-change due to using the expanded gap regions. Thanks to Pete Causey-Freeman for excellent examples that highlight the need for this: NC_000012.11:g.122064777_122064779del and NC_000003.11:g.14561629_14561630insG. refs #20948
• src/inc/dnautil.h
  • lines changed 3, context: html, text, full: html, text
    e9c75e7382c49565a3fae9791ab5da4f631debaa Mon Feb 12 11:02:58 2018 -0800
    In ad3a17645 I removed isAllDna from dnautil.c but not from dnautil.h - cleaned up now.