Commits for chmalee

v405_preview to v405_preview2 (2020-09-21 to 2020-09-28) v405

2ecc3d06e54d325c3e45850738ddd44b19f79a23 Tue Sep 22 07:41:43 2020 -0700

• Fix lovd short and long table names in autoSql, refs build email
  • src/hg/utils/otto/lovd/lovd.long.as - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/lovd/lovd.short.as - lines changed 1, context: html, text, full: html, text

f0cd304218bd294a3630f6d12f42325d3c6472d5 Tue Sep 22 11:24:43 2020 -0700

• Fix genome in a bottle structural variants build script to not fail when a field is missing from input
  • src/hg/utils/otto/dbVar/processNstd175.py - lines changed 6, context: html, text, full: html, text

cdf38279ca376913f58c332cbaeca92f573fc9bd Tue Sep 22 11:26:51 2020 -0700

• Keep dbVar otto scripts up to date
  • src/hg/utils/otto/dbVar/dbVarWrapper.sh - lines changed 1, context: html, text, full: html, text

d7258f3b93b43cac09ac69d4cf04aae663edf00a Tue Sep 22 16:12:09 2020 -0700

• Fixing typo in decipherSnvs stanza
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text

a3e03473bbde188141b61d0c3db48c85d2ec6aa3 Tue Sep 22 17:38:13 2020 -0700

• Basic vcf to bed converter, with a -fields argument for what VCF INFO tags to include in the bigBed itself, refs #25010
  • src/hg/hgc/vcfClick.c - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/vcfToBed/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/vcfToBed/vcfToBed.c - lines changed 282, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 13, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 26, context: html, text, full: html, text

13db5365510728c1e96d96110a6fe86065949b8a Thu Sep 24 16:17:54 2020 -0700

• Make vcfToBed way more basic and don't do any special parsing of VCF specific stuff, just chop out requested fields, refs #25010
  • src/hg/utils/vcfToBed/vcfToBed.c - lines changed 164, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 6, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text

1562b816fff70fb76a2c67341e5488c562e51857 Fri Sep 25 14:52:52 2020 -0700

• Code cleanup in vcfToBed and fix wrong array length variable for looping over info fields, refs #25010
  • src/hg/utils/vcfToBed/vcfToBed.c - lines changed 108, context: html, text, full: html, text