Commits for angie

v341_base to v342_preview (2016-11-07 to 2016-11-14) v342

6ee08e1c05fbac92e545429f446d75b441c6c370 Thu Nov 3 12:55:15 2016 -0700

• Fixing dependency so web.o is rebuilt when jWestBanner.h is rebuilt.
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text

07db8c7cc0e21b21c49d9d37502e12101e54b22d Fri Nov 11 20:10:36 2016 +0000

• Don't errAbort if an exon edge is not an exon-intron junction but instead an exon-exon junction -- i.e. an alignment gap for a deletion in the reference. The ideal way to annotate an insertion where the reference has a deletion is an open question.
  • src/hg/lib/gpFx.c - lines changed 4, context: html, text, full: html, text

a3616feb00b8f200afb7379d2f8e5fa3107eebd1 Fri Nov 11 20:05:02 2016 +0000

• Add -lz after htslib -- without it, couldn't link on GBiB.
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text

fe974de5e9ce0a6656ae862a851ff70967954a29 Fri Nov 11 18:42:01 2016 +0000

• Added env var JKTRASH so that when running on command line, trashDir can be something other than current directory.
  • src/lib/servcl.c - lines changed 16, context: html, text, full: html, text

b1c2fdec9a31078a56333427830a760757d22a51 Fri Jun 17 14:44:44 2016 -0700

• Command line wrapper script for hgVai: hg/utils/vai.pl . hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line. Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not). Has been tested somewhat on GBiB. Needs documentation. refs #12216
  • src/hg/hgVai/hgVai.c - lines changed 28, context: html, text, full: html, text
  • src/hg/inc/hAnno.h - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/pgSnp.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/variant.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/annoFormatVep.c - lines changed 26, context: html, text, full: html, text
  • src/hg/lib/annoGratorGpVar.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hAnno.c - lines changed 37, context: html, text, full: html, text
  • src/hg/lib/pgSnp.c - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/variant.c - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/vai.pl - lines changed 276, context: html, text, full: html, text