Commits for angie

v373_base to v374_preview (2018-10-22 to 2018-10-29) v374

ec80006d427f1d51d2d104ab7d1192ec2b2818a5 Mon Oct 22 15:53:23 2018 -0700

• Moving hgvsToVcf to userApp build, after a couple expressions of interest from external groups.
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text

48ff31d7c310549df1111e86dcd3abd66abe6586 Wed Oct 24 16:37:39 2018 -0700

• Alt haplotype and fix patch alignment tracks with links to multi-region mode (refs #18854) * Adding altSeqLiftOverPsl and fixSeqListOverPsl as top-level tracks (release alpha). * New 'db' option for baseColorUseSequence makes it fetch sequence from the current database (or other database if specified) -- we don't need seq/extFile for alts and patches now that they have been added to the .2bit. * Special hgc handler for {alt,fix}SeqLiftOverPsl has links to view the alt/fix in multi-region mode, to see the alignment details in the current position range, and to jump to the corresponding position range in the browser.
  • src/hg/hgTracks/cds.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 122, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/altSeqLiftOverPsl.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fixSeqLiftOverPsl.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 32, context: html, text, full: html, text