Commits for braney

v383_preview2 to v383_base (2019-06-03 to 2019-06-10) v383

90782cab70bd2f2ee992b0a7f95b656c56fdbba1 Mon Jun 3 15:34:47 2019 -0700

• order public hubs by shortLabel
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 25, context: html, text, full: html, text

620af6412b4ca31db9608d127ec4b25c3445955a Mon Jun 3 17:28:38 2019 -0700

• don't crash if a track specifies a group that doesn't exist in hgCollection
  • src/hg/hgCollection/hgCollection.c - lines changed 4, context: html, text, full: html, text

8933db12a9efed4981ada1fcc16e51a364147b0a Tue Jun 4 16:57:53 2019 -0700

• look for BAM index by just adding .bai to the end of the bam file, and if that does NOT work , try replacing the old suffix (presumably .bam) with .bai and try that. Also, we weren't adding the whole URL to bigDataIndex in hubs, so now we do.
  • src/hg/lib/trackHub.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 18, context: html, text, full: html, text

7466895f92735f9a050b7080214195124b37e226 Wed Jun 5 17:32:18 2019 -0700

• add fixStepToBedGraph.pl and varStepToBedGraph.pl to build so they'll appear in userApps
  • src/hg/makeDb/hgLoadWiggle/makefile - lines changed 7, context: html, text, full: html, text

3c53a67c75ff46566000137b4eb6dba7d1695b41 Thu Jun 6 09:05:40 2019 -0700

• added bisBis1 to hgwbeta.dbs and rr.dbs
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/rr.dbs - lines changed 1, context: html, text, full: html, text

8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700

• ongoing work on trackDb caching in shared memory
  • src/hg/inc/trackDb.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 20, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 70, context: html, text, full: html, text
  • src/inc/localmem.h - lines changed 6, context: html, text, full: html, text
  • src/lib/localmem.c - lines changed 18, context: html, text, full: html, text