Commits for hiram

v394_base to v395_preview (2020-02-17 to 2020-02-24) v395

22a9ec8b34dd60a14257bdef408f21c03db601b4 Mon Feb 17 16:06:38 2020 -0800

• now using the shorter assembly name for genome identifier and fix some common names refs #23891
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/makefile - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 5, context: html, text, full: html, text

b8652889568318e20760075bc46291560f93026a Mon Feb 17 16:07:32 2020 -0800

• using the shorter makefile procedure refs #23891
  • src/hg/makeDb/doc/vertebrateAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/mkList.sh - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.taxId.list - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.xrefName.list - lines changed 26, context: html, text, full: html, text

0503f0e3879f41dda5a9e6b807dd948fe910d745 Mon Feb 17 16:08:41 2020 -0800

• now using the shorter assembly identifer for genome name refs #23891
  • src/hg/makeDb/doc/birdsAsmHub/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/makefile - lines changed 3, context: html, text, full: html, text

ea52f7b77dacc8394101c6d841fcb845eec488c6 Mon Feb 17 16:11:16 2020 -0800

• moved to vertebrateAsmHub refs #23891
  • src/hg/makeDb/doc/vertebratesAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebratesAsmHub/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebratesAsmHub/mkList.sh - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.taxId.list - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.xrefName.list - lines changed 26, context: html, text, full: html, text

b453f8b92536b6c2280d2f02dc45150fc2d4cbcb Mon Feb 17 16:13:56 2020 -0800

• correct name for this hub.txt refs #23891
  • src/hg/makeDb/doc/mammalsAsmHub/hub.txt - lines changed 3, context: html, text, full: html, text

e576244638baffc0950375f9f7c14a392e93b193 Mon Feb 17 16:14:24 2020 -0800

• correct name for this hub.txt refs #23891
  • src/hg/makeDb/doc/primatesAsmHub/hub.txt - lines changed 1, context: html, text, full: html, text

ecc8358a1e03a67aba51417799cca013f98eacc5 Mon Feb 17 16:38:17 2020 -0800

• correct construction of name index file from the gtfToGenePred infoOut.txt newer format refs #23891
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 4, context: html, text, full: html, text

53d682e17e5ae17bd10a2f240178d05b4da9d0f4 Mon Feb 17 16:39:15 2020 -0800

• correct behavior for trackDb for ensGene track refs #23891
  • src/hg/utils/automation/asmHubEnsGene.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 17, context: html, text, full: html, text

ea8b0592fa84d8ea6a69ab9036609b4bdad4bd29 Tue Feb 18 15:12:25 2020 -0800

• need to have this genePredFilter do the elimination of illegal itesm instead of hgLoadGenePred for assembly hub track construction refs #24963
  • src/hg/utils/genePredFilter/genePredFilter.c - lines changed 14, context: html, text, full: html, text