Commits for hiram

v335_preview2 to v335_base (2016-06-27 to 2016-07-04) v335

e9a08f6fde15a5e1c734cf172010d6cec738003a Mon Jun 27 13:18:20 2016 -0700

• adding gorGor5 and moving all gorGor to primates.ra refs #17580
  
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 265, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 150, context: html, text, full: html, text

3d98fa29168afc1e3d54f91c396d4fcb1356e263 Mon Jun 27 13:59:16 2016 -0700

• adding gorGor5 to the composite Primate refs #17580
  
  • src/hg/makeDb/trackDb/human/chainNetGorGor4.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetGorGor5.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetLegacy.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 31, context: html, text, full: html, text

1f113a15a2cbcbdfeb4040188432cd3d013a57be Mon Jun 27 14:56:13 2016 -0700

• allow chain/net coloring of contig based assemblies with WGS naming schemes refs #17580
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 10, context: html, text, full: html, text
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text
  • src/lib/common.c - lines changed 18, context: html, text, full: html, text

52638bd89b284d3d524cc2a5d978032759a90c96 Mon Jun 27 15:41:46 2016 -0700

• do not need the regexHelper.h refs #1758
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

8e566fe74dab83fee7b705d1084871094065c68d Tue Jun 28 13:36:01 2016 -0700

• add print out of host name in error message about versioned js/style files no redmine
  
  • src/hg/lib/web.c - lines changed 4, context: html, text, full: html, text

a50ed53aff81d6fb3e34e6913ce18578292bc24e Tue Jun 28 15:00:42 2016 -0700

• implement an arbitrary 10-color palette scheme for scaffold/contig coloring refs #17580
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 30, context: html, text, full: html, text
  • src/hg/inc/chromColors.h - lines changed 49, context: html, text, full: html, text

d4cf4e65eee46690aba5e9128068b9ed3ac68c55 Wed Jun 29 10:05:13 2016 -0700

• lastz run hg38 to gorGor5 refs #17580
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 69, context: html, text, full: html, text

91b791ed4110a92f0b80c1ae73612f17e46846a3 Wed Jun 29 10:19:36 2016 -0700

• lastz runs per user request gorGor4 refs #17581
  
  • src/hg/makeDb/doc/hg18.txt - lines changed 71, context: html, text, full: html, text

2475f2b48ac1d5718541391f3338b151740b2787 Wed Jun 29 10:20:47 2016 -0700

• lastz runs per user request gorGor4 refs #17581
  
  • src/hg/makeDb/doc/panTro4.txt - lines changed 70, context: html, text, full: html, text

2554b2eb761e879f56893122daca7fe2e03c3ca5 Wed Jun 29 16:52:59 2016 -0700

• need -inclHap on the noClass.net file creation refs #16414
  
  • src/hg/makeDb/doc/mm10Patch4/mm10Patch4.txt - lines changed 8, context: html, text, full: html, text

1486e4871920562d08d0d4f03e220815d72a8e8d Thu Jun 30 15:48:03 2016 -0700

• fixup search rules for haplotypes and patches names refs #16414
  
  • src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra - lines changed 2, context: html, text, full: html, text

1fce3d03051ecda682f9d79aacdb56124cad06c3 Mon Jul 4 11:12:39 2016 -0700

• v335 final build refs #17576
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

2618c345307ad1f19a28d54865ed9709114978f7 Mon Jul 4 11:13:50 2016 -0700

• New version number v335
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text