Commits for hiram

v420_preview2 to v420_base (2021-08-30 to 2021-09-07) v420

cde87e3d79ee923945b80b85d708ab9d07475263 Wed Sep 1 13:26:02 2021 -0700

• improved bottleneck penalty for custom track loading even when they fail to load refs #28049
  • src/hg/lib/customTrack.c - lines changed 20, context: html, text, full: html, text

fb5a1a487756e0535aef78cf7818c7ea9c5f09e7 Wed Sep 1 15:21:45 2021 -0700

• using ram=16g on the cluster jobs to help prevent cluster job failures no redmine
  • src/hg/utils/automation/doTandemDup.pl - lines changed 13, context: html, text, full: html, text

1f92dad159673221d937c939cfabf4ac32534823 Wed Sep 1 15:22:44 2021 -0700

• use genePredFilter to eliminate the circular wrap around genes on chrMT and like chromosomes no redmine
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 4, context: html, text, full: html, text

9fb7e2a933dd0b378f251d348153730c9972ddcd Wed Sep 1 15:24:05 2021 -0700

• eliminate small errors in unlocalized scaffold names and genePredFilter for ncbiGene to eliminate problem gene definitions no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 8, context: html, text, full: html, text

054ce7806ed2e09aa1e24d1a126fedfb96bd1348 Thu Sep 2 14:22:15 2021 -0700

• show current botDelay millis after the ct loading penalty refs #28049
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text

8b6ee6734404f7ab681577f5044559dd2ce8bc08 Fri Sep 3 12:24:45 2021 -0700

• print heredoc need to have ; on the print line refs #23891
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 14, context: html, text, full: html, text

bc60ecbf3126d1c8502d28b45dde545bf8467d8b Fri Sep 3 15:14:40 2021 -0700

• not a good idea to add delay for zero custom tracks loaded, something in hgc is calling this repeatedly for no custom tracks refs #28049
  • src/hg/lib/customTrack.c - lines changed 1, context: html, text, full: html, text

4ff52b737cc301bc1f66518cdc6336c8b976bb16 Mon Sep 6 09:31:38 2021 -0700

• do not penalize for each custom track, just one penalty per submissiong refs #28049
  • src/hg/lib/customTrack.c - lines changed 4, context: html, text, full: html, text