Commits for braney

v335_preview to v335_preview2 (2016-06-20 to 2016-06-27) v335

3647e685aabe9799ce73695ac4e34b8d15891fc6 Tue Jun 21 06:51:25 2016 -0700

• add bigPsl to list of types which are bigBeds.
  
  • src/hg/inc/trackDb.h - lines changed 1, context: html, text, full: html, text

d6c8da3c30e51a633791c74318b4e42d5d76bd4d Tue Jun 21 11:20:34 2016 -0700

• a couple of changes to bigMaf support (no parallel load because of SQL
  access) and initialize some variables to avoid garbage memmory accesses.
  
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 3, context: html, text, full: html, text

abc3d457af89c9f05fccb4afdeac6be7b01908b2 Tue Jun 21 12:09:09 2016 -0700

• change hgGeneData to point to hgFixed.refSeqSummary
  
  • src/hg/hgGene/hgGeneData/Human/genome.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Mouse/genome.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Rat/genome.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Rat/rn3/genome.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Zebrafish/genome.ra - lines changed 2, context: html, text, full: html, text

43319b9d4967f68a609194350cd9e5a3458c183f Tue Jun 21 16:28:26 2016 -0700

• add hg38 knownGene blastTabs
  
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh - lines changed 44, context: html, text, full: html, text

f968102aae596db0a1677e583f10bf894845f596 Wed Jun 22 12:28:28 2016 -0700

• make ucsc genes on hg38 use a different set of assemblies for the "other
  orgs".
  
  • src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra - lines changed 20, context: html, text, full: html, text

a1ad78bcb6927c8bea0a98e530ff8a8771cccf03 Wed Jun 22 14:35:37 2016 -0700

• Replace the annoying cdsStartStat and cdsEndStat field descriptions in
  bigGenePred.as #17370
  
  • src/hg/hgc/hgc.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/bigGenePred.as - lines changed 2, context: html, text, full: html, text

21a6e23f42babbd11e4fae8f63f3e13afee5ab17 Wed Jun 22 17:40:53 2016 -0700

• fix up a query to dm6 in hgGeneData
  
  • src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra - lines changed 1, context: html, text, full: html, text

2c189392a8091ded2170963623a35d606da5f7da Wed Jun 22 20:01:55 2016 -0700

• a few mentions of refLink in hgGeneData
  
  • src/hg/hgGene/hgGeneData/Human/links.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/links.ra - lines changed 2, context: html, text, full: html, text

5af25d5af09cf586acbcf1c8a54d175deede25e7 Thu Jun 23 15:07:49 2016 -0700

• some tweaks in response to code review with Jonathan.
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
  • src/inc/bedTabix.h - lines changed 4, context: html, text, full: html, text
  • src/lib/bedTabix.c - lines changed 12, context: html, text, full: html, text

0659fd086f068d8757dd716d12a8dd572a7de846 Fri Jun 24 12:38:05 2016 -0700

• fix HTML error in table browser if track doesn't support intersections
  
  • src/hg/hgTables/mainPage.c - lines changed 3, context: html, text, full: html, text