Commits for angie

v364_preview to v364_preview2 (2018-04-02 to 2018-04-09) v364

7cdc9f476f19a65d36e015aadf41be9634e15920 Wed Apr 4 11:45:43 2018 -0700

• For genePred tracks, limit baseColorDrawOpt to genomicCodons if it's set to a fancy PSL option because the setting comes from a view that includes a PSL track. refs #21194
  • src/hg/lib/hui.c - lines changed 11, context: html, text, full: html, text

74bbd952e4cb5fef80030a534ec6b714bc561adb Wed Apr 4 14:38:30 2018 -0700

• Use hasAltAllele to determine what soTerm to use in aggvGenelessRow. Thanks Jonathan! refs #21204
  • src/hg/lib/annoGratorGpVar.c - lines changed 3, context: html, text, full: html, text

5780fed8b94b69b4b22e2d389112e4d34d51368f Fri Apr 6 09:31:50 2018 -0700

• Fixing lack of NULL checks on result of vcfFileName. Symptom was crash on tgpPhase3 which has no file for chrM when doing genome-wide query. refs #21218
  • src/hg/hgTables/vcf.c - lines changed 15, context: html, text, full: html, text

1bf3b778f91427db8eee4c35397ada236a9a2b35 Fri Apr 6 13:35:22 2018 -0700

• Remove zebrafish-specific pattern so this can be used on other species; use python instead of shell commands to extract information from inputFile, find alt AGP files, and build altChrmList.
  • src/hg/utils/automation/ucscAltAgp - lines changed 40, context: html, text, full: html, text