Commits for braney

v419_base to v420_preview (2021-08-16 to 2021-08-23) v420

99956f21187562fe5f789185a150b9b9dbde7b01 Mon Aug 16 14:46:03 2021 -0700

• make sure a stack variable is initialized. #27801
  • src/hg/hgc/rnaFoldClick.c - lines changed 1, context: html, text, full: html, text

d0aad7f66c2fee0fa9366c3b3caf4d761750c055 Tue Aug 17 10:27:07 2021 -0700

• first version of Gencode genes (knownGene version) for mm39
  • src/hg/hgGene/hgGeneData/Mouse/mm39/links.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Mouse/mm39/otherOrgs.ra - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/doHgNearBlastp.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildBioCyc.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildBlast.sh - lines changed 123, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildCgap.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildCore.sh - lines changed 56, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildCore.sh.safe - lines changed 208, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildEnv.sh - lines changed 49, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildFoldUtr.sh - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildKegg.sh - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildKnown.sh - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildPfamScop.sh - lines changed 101, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildTo.sh - lines changed 48, context: html, text, full: html, text

7c5f089c583b6a7ff0439109000eb121e6ff5d8b Tue Aug 17 14:50:36 2021 -0700

• build the knownGene and knownCanonical mafGene downloads
  • src/hg/utils/otto/knownGene/buildMafGene.sh - lines changed 96, context: html, text, full: html, text

0d7eae2999eedc95d9205d915feec3575e783849 Wed Aug 18 12:42:35 2021 -0700

• html for mm39 knownGene
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.html - lines changed 142, context: html, text, full: html, text

2f81eb835c8cffd5ba9937cec91b3a0f1c64541d Wed Aug 18 14:47:31 2021 -0700

• fixed a usage message and added a makefile for the tests in cartEditSuperTrack.c
  • src/hg/utils/cartEditSuperTrack/cartEditSuperTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/cartEditSuperTrack/tests/makefile - lines changed 19, context: html, text, full: html, text

776afaa6ba708aed97b79ceccb2a445e129b2f4c Thu Aug 19 12:44:36 2021 -0700

• add a hReplaceGbdb() for knownGene fast search
  • src/hg/lib/hgFind.c - lines changed 1, context: html, text, full: html, text

c2204b34508ac64160836ae01a16fe3f2baa3fd8 Thu Aug 19 13:25:45 2021 -0700

• don't assume LRG bigBed is local cuz that will fail on GBiB
  • src/hg/lib/hgHgvs.c - lines changed 1, context: html, text, full: html, text

2b6c6b0a93928d762a71612a7b2be14aba56c436 Thu Aug 19 14:53:02 2021 -0700

• we need to replace /gbdb with hgdownload: addresses on gBiB. refs #28109
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hAnno.c - lines changed 3, context: html, text, full: html, text

767f6d5f100faf63370d0a0c317db0311c055d64 Thu Aug 19 16:20:12 2021 -0700

• update dbCount when updating dbList in the hubPublic table
  • src/hg/utils/hubPublicCheck/hubPublicCheck.c - lines changed 10, context: html, text, full: html, text

4ddbd4de63bff1948c81c6b84aa9334cdadeeb8c Fri Aug 20 17:48:25 2021 -0700

• restore the watermark in the position box if we update the hgTracks image. refs #27728
  • src/hg/js/autocomplete.js - lines changed 36, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 3, context: html, text, full: html, text