Commits for angie

v356_base to v357_preview (2017-10-09 to 2017-10-16) v357

e5bca336b3a879884c7cd865cc2c1758e5ffbb3e Fri Oct 13 14:32:01 2017 -0700

• Check for NULL to support VCF files with missing header definitions.
  • src/hg/hgc/vcfClick.c - lines changed 1, context: html, text, full: html, text

ec16665b0cbbc7f8e01992a65d328bee629b4e01 Fri Oct 13 15:01:12 2017 -0700

• Multi-base substitutions that straddled codon boundary were incompletely reported in {codon,aa}{Old,New} fields. fixes #20327
  • src/hg/lib/gpFx.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 1, context: html, text, full: html, text

34b00a6ec9f42cc2c1d16e43e571c67e800e0604 Fri Oct 13 16:18:11 2017 -0700

• Fix error that caused insertion between splice site and the rest of the splice region to fall through the conditions for splice_region. fixes #20328.
  • src/hg/lib/gpFx.c - lines changed 2, context: html, text, full: html, text

1c81d5ea61946f0fe68315a4679d68a4f3baf0f4 Fri Oct 13 17:00:50 2017 -0700

• Oops, forgot to reverse-complement shifted genomic sequence when transcript is on - strand. fixes #20329
  • src/hg/lib/variantProjector.c - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab - lines changed 1, context: html, text, full: html, text