File Changes for angie

v360_base to v361_preview (2018-01-22 to 2018-01-29) v361

• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    f0aa2132b515869f610cef5a880789875eb2c3e0 Sat Jan 27 10:36:42 2018 -0800
    Minor inefficiency when generating VCF from dbSNP IDs: refAl is trimmed from "-" to "", so when altAl "-" was compared to refAl it differed, causing the reference allele to appear redundantly in the alt alleles column. So trim altAl "-" to "" before comparing for consistency.
• src/hg/inc/annoStreamDbPslPlus.h
  • lines changed 24, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
• src/hg/inc/gpFx.h
  • lines changed 19, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/inc/joiner.h
  • lines changed 9, context: html, text, full: html, text
    78fd01e7d81e12b132a1a9d2238015c67e25475f Thu Sep 28 10:02:48 2017 -0700
    Added option to structure joinerPair routeList as a tree using joinerPairListToTree() and new child pointer, so that if one pair's b is the same table as another pair's a, the second pair becomes the child of the first pair. This enables us to generate more efficient SQL joins.
• src/hg/inc/soTerm.h
  • lines changed 2, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/inc/variantProjector.h
  • lines changed 17, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/annoFormatVep.c
  • lines changed 90, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 314, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/annoStreamDb.c
  • lines changed 38, context: html, text, full: html, text
    c54488382199f754b2226109da2995eb16dff19b Thu Sep 28 10:06:31 2017 -0700
    Call joinerPairListToTree on sqlRouteList and use tree structure to make more efficient joins. Also use 'full' keyword to do joins instead of left joins (more efficient).
  • lines changed 25, context: html, text, full: html, text
    869708731727a455813ab88e67d46be978ab77b0 Fri Jan 12 14:48:37 2018 -0800
    Added new config parameters rightJoinDtf and rightJoinMainField to give the option of limiting rows to those that join with some other table. The motivation for this is wanting to get only the rows of ncbiRefSeqPsl that join with ncbiRefSeqCurated.
• src/hg/lib/annoStreamDbPslPlus.c
  • lines changed 185, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
  • lines changed 3, context: html, text, full: html, text
    dd285f81141e45dabf1caf0f90723810f2c6f8a1 Fri Jan 12 14:50:04 2018 -0800
    Use the new annoStreamDb params rightJoinDtf and rightJoinMainField to restrict ncbiRefSeqPsl rows to only those that appear in the selected genePred table (e.g. ncbiRefSeqCurated).
• src/hg/lib/gpFx.c
  • lines changed 82, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/hAnno.c
  • lines changed 14, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/hgHgvs.c
  • lines changed 14, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/joiner.c
  • lines changed 58, context: html, text, full: html, text
    78fd01e7d81e12b132a1a9d2238015c67e25475f Thu Sep 28 10:02:48 2017 -0700
    Added option to structure joinerPair routeList as a tree using joinerPairListToTree() and new child pointer, so that if one pair's b is the same table as another pair's a, the second pair becomes the child of the first pair. This enables us to generate more efficient SQL joins.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
• src/hg/lib/soTerm.c
  • lines changed 2, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 36, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 8, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/variant.c
  • lines changed 49, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/variantProjector.c
  • lines changed 805, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/makeDb/schema/joinerRoute/joinerRoute.c
  • lines changed 72, context: html, text, full: html, text
    a842f599b275e1b92a826ce0c6812711a646eef3 Thu Sep 28 10:13:25 2017 -0700
    joinerRoute: util to display the paths that joinerFindRouteThroughAll finds to join a list of tables. Sometimes it's not what you'd expect and you may want to tweak all.joiner.
• src/hg/makeDb/schema/joinerRoute/makefile
  • lines changed 3, context: html, text, full: html, text
    a842f599b275e1b92a826ce0c6812711a646eef3 Thu Sep 28 10:13:25 2017 -0700
    joinerRoute: util to display the paths that joinerFindRouteThroughAll finds to join a list of tables. Sometimes it's not what you'd expect and you may want to tweak all.joiner.
• src/lib/vcf.c
  • lines changed 18, context: html, text, full: html, text
    675a334117c7a98be59035fdf620ac8ca764fd1e Thu Jan 18 12:11:33 2018 -0800
    isAllNt ignores last base in string so beware; also, isAllNt returns true for "-" (translates it to 'n') but that means the empty string so exclude it from base-trimming.
  • lines changed 21, context: html, text, full: html, text
    e38dd775f9552b3d050b6910c0989be5aba715f1 Fri Jan 19 12:54:23 2018 -0800
    'Variants' with no alternate allele may come in two forms: alt == '.' or alt == ref. In either case, filter down to ref only.