Commits for hiram

v367_preview2 to v367_base (2018-06-11 to 2018-06-18) v367

b6a4584ec8b42d2975e2fd81962d7d67506d42c8 Mon Jun 11 10:05:20 2018 -0700

• adding patch13 to hg19 refs #9869
  • src/hg/makeDb/trackDb/human/hg19/hg19Patch13.html - lines changed 1065, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text

deb448760014f007f153baebb29f5a8007c3ed0b Mon Jun 11 10:06:10 2018 -0700

• adding patch13 to hg19 refs #9869
  • src/hg/makeDb/doc/hg19Patch13.txt - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19PatchDescr.pl - lines changed 120, context: html, text, full: html, text

1f736c9167f033fa13f21da36d510d609bfa63e4 Mon Jun 11 10:40:23 2018 -0700

• adding chainNet to equCab3 refs #21223
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 13, context: html, text, full: html, text

6523ada01fa1e1a6e4167019b7cd63607609f20c Mon Jun 11 15:44:57 2018 -0700

• completed QA ready refs #21223
  • src/hg/makeDb/doc/equCab3/initialBuild.txt - lines changed 62, context: html, text, full: html, text

83dfbdfee5e4c07370df74066e6f657df47250d0 Wed Jun 13 09:26:25 2018 -0700

• lastz chainNet to balAcu1 per user request refs #21583
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 82, context: html, text, full: html, text

8fa409541ae77d8b6cd9bcc5bf5525f7a3f59502 Wed Jun 13 09:39:19 2018 -0700

• only use cluster hub for partition if blastzOutRoot option given, otherwise workhorse is the ticket refs #21583
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

723a5385f843cecfea3a840522bc5aa36b9b94be Wed Jun 13 10:25:49 2018 -0700

• adding gold/assembly search rule refs #21583
  • src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra - lines changed 6, context: html, text, full: html, text

230b9662b6cad6121017880b076fd8d40fecc269 Wed Jun 13 11:06:40 2018 -0700

• add gold assembly search rule and lastz to hg38 refs #21583
  • src/hg/makeDb/doc/balAcu1.txt - lines changed 68, context: html, text, full: html, text

646b0caf1807041c0407418fb0fceca137078731 Wed Jun 13 11:15:44 2018 -0700

• adding Minke whale balAcu1 definitions refs #21583
  • src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra - lines changed 59, context: html, text, full: html, text

3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700

• added information to usage output and add test example for inclusion in userApps refs #21617
  • src/utils/cpgIslandExt/cpg_lh.c - lines changed 25, context: html, text, full: html, text
  • src/utils/cpgIslandExt/tests/expected.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/cpgIslandExt/tests/makefile - lines changed 6, context: html, text, full: html, text
  • src/utils/cpgIslandExt/tests/test.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/utils/cpgIslandExt/tests/test.sh - lines changed 11, context: html, text, full: html, text

0d55c5beaf3c8c6f8b522959c49a57ec8800cde3 Thu Jun 14 10:46:33 2018 -0700

• adding cpgIslandExt to userApps refs #21617
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

b203f2127214a1836d9db90028d65dece8482197 Thu Jun 14 12:07:12 2018 -0700

• add balAcu1 lastz chainNet refs #21583
  • src/hg/makeDb/doc/mm10.txt - lines changed 75, context: html, text, full: html, text

377405f8eb685657879db8eb6a19be5ccb0714c7 Thu Jun 14 16:02:39 2018 -0700

• for 3-way alignment on micMur3 no redmine
  • src/hg/htdocs/images/phylo/micMur3_3way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

34d88003b0e7eccd3293db920077b7a3dfdd723b Thu Jun 14 16:15:23 2018 -0700

• incorrect item on top no redmine
  • src/hg/htdocs/images/phylo/micMur3_3way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

479634cda34febfcf8594e24f222d5e9cd6aa8ab Thu Jun 14 18:23:48 2018 -0700

• running up 3-way on micMur3 no redmine
  • src/hg/makeDb/doc/micMur3/multiz3way.txt - lines changed 1416, context: html, text, full: html, text

2dda61d8163344f7a6f8c65a32e244431117f132 Fri Jun 15 16:33:03 2018 -0700

• adding 3-way conservation no redmine
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html - lines changed 413, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.3way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra - lines changed 3, context: html, text, full: html, text

c2210b6df23631c05b4725a60a4b3ff0c1b0bb75 Fri Jun 15 17:00:02 2018 -0700

• correct view limits on the phyloP track no redmine
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.3way.ra - lines changed 3, context: html, text, full: html, text

b5a75fbe3b5f2ba9102e852c27161c880a39a0b3 Fri Jun 15 17:00:52 2018 -0700

• 3-way alignment complete no redmine
  • src/hg/makeDb/doc/micMur3/multiz3way.txt - lines changed 179, context: html, text, full: html, text

66d0b28345df340070498839c4431bfaccc6e701 Fri Jun 15 17:01:33 2018 -0700

• 3-way alignment complete no redmine
  • src/hg/makeDb/doc/micMur3/multiz3way.txt - lines changed 14, context: html, text, full: html, text

7f20e528d9895bfc997b25cf28aa589b963fb7d4 Mon Jun 18 10:14:06 2018 -0700

• v367 final build, refs #21564
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

46c6b163494aff7c1726068b62418494b7fe9fe7 Mon Jun 18 10:18:33 2018 -0700

• New version number v367
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text