Commits for angie

v349_preview2 to v349_base (2017-05-08 to 2017-05-15) v349

cc6ca259385f385c252b6a675801025e96783818 Thu May 11 12:40:15 2017 -0700

• Converting HGVS coords to 0-based needs to be done differently when the HGVS coords are negative because when negative they are already 0-based (but end is closed and needs to be converted to open). fixes #19396
  • src/hg/lib/hgHgvs.c - lines changed 45, context: html, text, full: html, text

b7b52acb53114733301bf8fd23d269c6178518ab Fri May 12 14:08:54 2017 -0700

• Oops, hgvsToVcf (and any program that needs RefSeq/GenBank stuff) needs to call initGenbankTableNames().
  • src/hg/utils/hgvsToVcf/hgvsToVcf.c - lines changed 2, context: html, text, full: html, text

2bff6bdbbce7e4ef57b27d4104a12a076dc90ca5 Fri May 12 14:12:45 2017 -0700

• gbSeqTable doesn't work as compatTable for hGenBankGet* -- wrong columns. Also recognize indel when no-change in HGVS transcript term aligns to a deletion in reference. We're not yet showing the correct alt sequence in that case.
  • src/hg/lib/hgHgvs.c - lines changed 7, context: html, text, full: html, text