Commits for angie

v362_base to v363_preview (2018-03-05 to 2018-03-12) v363

a6177bc07e5dbb520e06cd0b341036efc2ecd3b3 Tue Mar 6 14:23:29 2018 -0800

• In hgFind, when adding a highlight via URL that the user clicks on, use a new cart variable addHighlight instead of appending to the current highlight string because that can get too long for a URL. refs #21056
  • src/hg/hgTracks/hgTracks.c - lines changed 26, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 20, context: html, text, full: html, text

ef39e447f159ff068789ce02e4a658b7bad9caec Wed Mar 7 16:15:27 2018 -0800

• checkAddHighlight also needs to be run after tracksDisplay because it may call findGenomePos which may set addHighlight again. refs #21056
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text

bc3bbb2794e3067f0ff35ac2003fd69362e2ed58 Thu Mar 8 11:34:17 2018 -0800

• Libified genePredToFakePsl's code for extracting PSL and CDS from genePred so I can use it to infer PSL+CDS from genePred tracks like Gencode for HGVS. refs #21076
  • src/hg/genePredToFakePsl/genePredToFakePsl.c - lines changed 67, context: html, text, full: html, text
  • src/hg/inc/genePred.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/genePred.c - lines changed 74, context: html, text, full: html, text

5f9ba1691bd3051146f2f9464c9d1375e42f6ff4 Thu Mar 8 11:36:57 2018 -0800

• Added support for ENS*T* transcript IDs in HGVS position search, using the latest Gencode. Added support for parsing ENS*P* protein IDs, but can't yet map those to the genome because our Gencode tables don't yet include a mapping between transcript and protein IDs. refs #21076
  • src/hg/inc/hdb.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 50, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/hgHgvs.c - lines changed 339, context: html, text, full: html, text

31744b6e479fbe5e49b3188e651a328cf3374ed0 Thu Mar 8 13:40:51 2018 -0800

• Added support for ENS*P* accessions in HGVS position search. Thanks Mark for the new Attrs proteinId column! refs #21076
  • src/hg/lib/hgHgvs.c - lines changed 108, context: html, text, full: html, text

27f4b613573c4688872ccebd6260e5aefce86ac4 Thu Mar 8 13:59:34 2018 -0800

• wgEncodeGencodeAttrsLoad needs its new argument in a couple more places.
  • src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 1, context: html, text, full: html, text