Commits for hiram

v341_preview2 to v341_base (2016-10-31 to 2016-11-07) v341

bed79fc1964b5e7f176df34bbdf5d6675bc9a28b Tue Nov 1 10:49:34 2016 -0700

• to fixup extraction of source identity from Ensembl gtf file refs #18240
  • src/hg/utils/automation/extractSource.pl - lines changed 44, context: html, text, full: html, text

910034e3ec1547b950e6434a7a98486ddb4cb5d9 Tue Nov 1 11:21:52 2016 -0700

• description page for RNA Seq Star tracks, a copy of this file is in each species html directory refs #13553
  • src/hg/makeDb/doc/mouseStrains/rnaSeqStar.html - lines changed 190, context: html, text, full: html, text

0684c7b8dc207944939299c15c37aa8356a90fbb Tue Nov 1 12:52:03 2016 -0700

• no Gene Tree link on non-coding genes refs #18240
  • src/hg/hgc/hgc.c - lines changed 3, context: html, text, full: html, text

edba1b0991019bb90d73debfc028fcdc28f4e5b4 Tue Nov 1 14:06:34 2016 -0700

• for droSim2 browser wikimedia commons Dr Andrew Weeks https://commons.wikimedia.org/wiki/File:Drosophila_simulans-female.jpg refs #18269
  • src/hg/htdocs/images/Drosophila_simulans.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

a500c95137dd448e2d073e240ff1e02a323cfdb5 Tue Nov 1 14:35:12 2016 -0700

• adding droSim2 to the build refs #18269
  • src/hg/makeDb/trackDb/drosophila/droSim2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droSim2/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droSim2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droSim2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

aa99224331a34949e02ff3cc8942da2fd161ef3b Wed Nov 2 10:59:38 2016 -0700

• liftOver to droSim2 per user request refs #18269
  • src/hg/makeDb/doc/dm3.txt - lines changed 69, context: html, text, full: html, text

826af23bad85f06440c75d2f226160f0f21eaab2 Wed Nov 2 11:05:39 2016 -0700

• liftOver to droSim2 refs #18269
  • src/hg/makeDb/doc/droSim1.txt - lines changed 15, context: html, text, full: html, text

653888d85818c108e9505c4d0ec4f801c459128b Wed Nov 2 11:06:51 2016 -0700

• to construct dm3 to droSim2 liftOver refs #18269
  • src/hg/makeDb/doc/droSim2/initialBuild.txt - lines changed 564, context: html, text, full: html, text

196d206a199ee47dc303b5ddf54170f89e4daa75 Thu Nov 3 17:13:25 2016 -0700

• correctly counting matches and mis matches refs #13673
  • src/lib/bamFile.c - lines changed 5, context: html, text, full: html, text

2bd5caf8ce518d13cefc69de0d084228cf7712fe Fri Nov 4 13:36:48 2016 -0700

• adding useful options refs #13673
  • src/utils/bamToPsl/bamToPsl.c - lines changed 90, context: html, text, full: html, text

93115ea6e9d63814f717023f1e798d1025ad494c Fri Nov 4 13:37:30 2016 -0700

• adding bamToPsl to utils refs #13673
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

47802304b1952dbda253f7b3c9d17cf0f8bf2d2e Sat Nov 5 14:14:30 2016 -0700

• adding build notes refs #13553
  • src/hg/makeDb/doc/mouseStrains/mouseStrainsBuildNotes.txt - lines changed 84, context: html, text, full: html, text

82cec746b350c7a69784e7f66959b36351c2ce14 Mon Nov 7 09:36:27 2016 -0800

• the genomes.txt file refs #13553
  • src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt - lines changed 160, context: html, text, full: html, text

5c72520bca3d8ba7f0fe49ed1f1b8b473142a3ed Mon Nov 7 09:44:49 2016 -0800

• the groups.txt file for the mouse strains refs #13553
  • src/hg/makeDb/doc/mouseStrains/groups.txt - lines changed 39, context: html, text, full: html, text

43fd5b317fb16c32cf2895b70051c82fc4088e50 Mon Nov 7 09:53:41 2016 -0800

• adding blat servers refs #13553
  • src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt - lines changed 33, context: html, text, full: html, text

a08ce839f61a97d23b493640d7510ad13341990f Mon Nov 7 09:54:38 2016 -0800

• adding blat servers refs #13553
  • src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt - lines changed 1, context: html, text, full: html, text

8b5a8239d2432475ec19002c09963f7d3956de03 Mon Nov 7 10:05:28 2016 -0800

• v341 final build refs #18302
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

a1494fec288ca82de0a42c1f6315412fba7a154a Mon Nov 7 10:06:28 2016 -0800

• New version number v341
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text