Commits for angie

v353_base to v354_preview (2017-08-07 to 2017-08-14) v354

812dec9c5d8a5c947bd30442feae4a4449f50257 Wed Aug 9 13:41:58 2017 -0700

• Oops, forgot to handle '=' in hgvsParseNucleotideChange.
  • src/hg/lib/hgHgvsParse.c - lines changed 3, context: html, text, full: html, text

37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700

• Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
  • src/hg/inc/hdb.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 39, context: html, text, full: html, text
  • src/inc/common.h - lines changed 4, context: html, text, full: html, text
  • src/inc/dnaseq.h - lines changed 7, context: html, text, full: html, text
  • src/inc/dnautil.h - lines changed 7, context: html, text, full: html, text
  • src/lib/common.c - lines changed 23, context: html, text, full: html, text
  • src/lib/dnaseq.c - lines changed 27, context: html, text, full: html, text
  • src/lib/dnautil.c - lines changed 55, context: html, text, full: html, text

61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700

• New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
  • src/hg/inc/indelShift.h - lines changed 39, context: html, text, full: html, text
  • src/hg/inc/seqWindow.h - lines changed 53, context: html, text, full: html, text
  • src/hg/inc/variantProjector.h - lines changed 121, context: html, text, full: html, text
  • src/hg/lib/indelShift.c - lines changed 217, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/seqWindow.c - lines changed 141, context: html, text, full: html, text
  • src/hg/lib/variantProjector.c - lines changed 662, context: html, text, full: html, text

de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700

• Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
  • src/hg/hgVai/hgVai.c - lines changed 47, context: html, text, full: html, text
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/annoGratorGpVar.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/hgHgvs.h - lines changed 43, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 29, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 230, context: html, text, full: html, text
  • src/hg/lib/hgHgvs.c - lines changed 692, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 1, context: html, text, full: html, text

e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700

• new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
  • src/hg/utils/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab - lines changed 473, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab - lines changed 30, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_agree.vcf - lines changed 128, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf - lines changed 48, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/makefile - lines changed 29, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/vcfToHgvs.c - lines changed 319, context: html, text, full: html, text

efc5d694c63bb43de24814a20506798fb60b73ae Wed Aug 9 14:49:54 2017 -0700

• wiggleCart: Use theCart arg instead of global cart because not all mains define cart.
  • src/hg/lib/wiggleCart.c - lines changed 3, context: html, text, full: html, text

904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700

• Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
  • src/hg/lib/hgHgvs.c - lines changed 40, context: html, text, full: html, text
  • src/hg/lib/variantProjector.c - lines changed 31, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab - lines changed 46, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/input/stopLoss.vcf - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/makefile - lines changed 5, context: html, text, full: html, text