Commits for angie

v354_preview to v354_preview2 (2017-08-14 to 2017-08-18) v354

3712ae6f8f6f212bae33ecc5499feeea598d83e4 Mon Aug 14 11:52:33 2017 -0700

• HGVS pos/search: support parentheses around p. terms. Also watch out for start>end in hgvsValidateGene. refs #19968 note-6
  • src/hg/lib/hgHgvs.c - lines changed 18, context: html, text, full: html, text

bc5f960c316fcd863ff01af154b8bd67a4dc041a Mon Aug 14 15:08:45 2017 -0700

• hgVai: offer HGVS output options only when using RefSeq transcripts. refs #19968 note-8
  • src/hg/hgVai/hgVai.c - lines changed 30, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 4, context: html, text, full: html, text

1cd0b7c223ef9944459fbbdac10e3c21ab8a6edd Mon Aug 14 15:41:40 2017 -0700

• Oops, suppress HGVS output (not just options) when using non-RefSeq transcripts. refs #19968
  • src/hg/hgVai/hgVai.c - lines changed 5, context: html, text, full: html, text

3556696ddf8ee9dadf75805726fb2a4c226c7f92 Thu Aug 17 09:39:46 2017 -0700

• A little refactoring of logic that allows HGVS output only for RefSeq transcripts.
  • src/hg/hgVai/hgVai.c - lines changed 12, context: html, text, full: html, text

499eb9facae2cd13591dad0256751b9742aa1bea Thu Aug 17 09:52:36 2017 -0700

• Added asColumnMustFindIx. Use it in hgVai in places where columns are expected to never go away, instead of risking that they do go away and we access row[-1]. Thx Jonathan. refs #19992 note-13
  • src/hg/lib/annoFormatVep.c - lines changed 58, context: html, text, full: html, text
  • src/inc/asParse.h - lines changed 4, context: html, text, full: html, text
  • src/lib/asParse.c - lines changed 10, context: html, text, full: html, text

411050bf65e0240780f2657eaaee9fa92c263b59 Thu Aug 17 10:22:45 2017 -0700

• Removing abandoned experimental CGI hgVarAnnogrator. refs #19992 note-11
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 1805, context: html, text, full: html, text
  • src/hg/hgVarAnnogrator/makefile - lines changed 16, context: html, text, full: html, text

ea71930e7ad82f81fc98d619d39a5ac53ed55240 Thu Aug 17 10:50:50 2017 -0700

• Long-overdue renaming of hgVarAnnogrator.js to hgVai.js and removal of vestigial code. Thx Jonathan. refs #19992 note-11
  • src/hg/hgVai/hgVai.c - lines changed 1, context: html, text, full: html, text
  • src/hg/js/hgVai.js - lines changed 154, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 618, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text

5964a18a24a5531f2d14eb1be5c30bca115edc44 Fri Aug 18 07:41:09 2017 -0700

• RefSeq transcript updates caused diff failure... need a stable PSL+CDS+sequence test set.
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab - lines changed 4, context: html, text, full: html, text