File Changes for angie

v361_preview to v361_preview2 (2018-01-29 to 2018-02-05) v361

• src/hg/hgTables/vcf.c
  • lines changed 15, context: html, text, full: html, text
    a29e98e451251954d3c79928eda4ea4111f11151 Tue Jan 30 14:34:52 2018 -0800
    hgTables vcfFileName wasn't handling plain VCF custom tracks correctly.
• src/hg/lib/variantProjector.c
  • lines changed 4, context: html, text, full: html, text
    47f7e3e01a4acd51d8114c79880b6496f7b290a5 Mon Jan 29 15:57:30 2018 -0800
    spliceInBlk was demanding positive overlap between region/variant and block, but region and variant can be 0-length insertion points.
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    5cf6d3bf319a850cac1bd51c0b71ba016add589c Thu Feb 1 14:17:34 2018 -0800
    Added more accurate exon/intron/CDS predictions for complex variants (those that span multiple regions). Still need to catch transcript_ablation and splice_region_variant in vpTxToFxExon. HGVSP should reflect when the whole transcript has been deleted (IMO anyway).
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    c537ea714a6d43e286175be9e713bb7aff9bef72 Sun Feb 4 22:42:35 2018 -0800
    The previous change caused vpTranscriptToProtein to make predictions when it really shouldn't, e.g. for a purely intronic variant (or even for a variant that probably wipes out a splice site and extends into the exon). What I really want to add support for is complete transcript deletions -- so bring back the previous restrictive check and add an exception for complete deletions (start upstream, end downstream).
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    d8164d0a9702a2b3d4e20cd2afc0cee6f5ee0275 Fri Feb 2 15:26:47 2018 -0800
    Detect transcript_ablation and splice_region_variant in vpTxToFxExon.
• src/hg/mouseStuff/chainToPsl/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/genePredFilter/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/genePredToProt/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/pslRc/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/pslToBigPsl/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/hg/utils/transMapPslToGenePred/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/utils/bamToPsl/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.
• src/utils/bedClip/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    db612805d3cb5b69b52fd0e287638a7caedf6b21 Mon Jan 29 17:40:03 2018 -0800
    Clean up after 'make test'.