Commits for hiram

v358_preview2 to v358_base (2017-11-13 to 2017-11-27) v358

ebb367f7a4871a28b79b667f7c6eafbe892b647c Tue Nov 14 09:05:24 2017 -0800

• lastz chainNet to gorGor5 per user request refs #20482
  • src/hg/makeDb/doc/hg19.txt - lines changed 88, context: html, text, full: html, text

eef67ffcd89a88116d32c3548a99858104743f83 Tue Nov 14 11:01:34 2017 -0800

• turn on NCBI RefSeq for evaluation refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra - lines changed 2, context: html, text, full: html, text

626a6375905120ccf7e821f9927561d47a8a0bb9 Tue Nov 14 11:04:11 2017 -0800

• NCBI RefSeq on for only alpha make refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra - lines changed 1, context: html, text, full: html, text

52f4ca22edbec229dbac490a4fc6123044dad754 Tue Nov 14 11:06:20 2017 -0800

• adding lineLimit option to error out when files are too large no redmine
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 8, context: html, text, full: html, text

7783dc22842c5459e44bc3c861800a8e7588aa77 Tue Nov 14 11:15:10 2017 -0800

• turning on limit of 50 million lines for a bed file input to a custom track to eliminate the gigantic incoming files no redmine
  • src/hg/lib/customFactory.c - lines changed 3, context: html, text, full: html, text

aecff87074bb35effb6ee1620132f69466807409 Tue Nov 14 11:18:57 2017 -0800

• change the variable name warn to warnMsg to avoid clash with same name function no redmine
  • src/hg/hgCustom/hgCustom.c - lines changed 16, context: html, text, full: html, text

b9be85ef317a960033bc2cbaadf5a9b931c20061 Tue Nov 14 12:52:17 2017 -0800

• trying out a srcVersion print in optionsInit() no redmine
  • src/inc/srcVersion.h - lines changed 3, context: html, text, full: html, text
  • src/lib/options.c - lines changed 3, context: html, text, full: html, text

f1d847f8a1ccfcb1c1f7267e5f87e819bdfa4a2a Tue Nov 14 13:00:04 2017 -0800

• also edit the srcVersion.h file with the versionInfo.h no redmine
  • src/utils/qa/weeklybld/updateCgiVersion.csh - lines changed 3, context: html, text, full: html, text

6fdd5908880d6a2fb2e4f7235679981888d8055b Tue Nov 14 13:37:59 2017 -0800

• avoid verbose argument on a few commands no redmine
  • src/utils/userApps/mkREADME.sh - lines changed 9, context: html, text, full: html, text

50f1ff191f99e85d8f8ef21785fd27d142edec67 Tue Nov 14 14:17:46 2017 -0800

• a couple more programs that can not manage verbose argument no redmine
  • src/utils/userApps/mkREADME.sh - lines changed 1, context: html, text, full: html, text

3da2c082ae7d96244d1f2c0b78334623e45240a2 Tue Nov 14 14:27:59 2017 -0800

• note featureBits for gorGor5 chainRBestHg19 refs #20482
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text

8621d381fa72623be321c96e4ac19e652a01147a Tue Nov 14 14:37:14 2017 -0800

• eliminate one ERROR: message no redmine
  • src/utils/userApps/mkREADME.sh - lines changed 1, context: html, text, full: html, text

cfb24cb7ed14b50c6a6ff273be7929ff345716d6 Tue Nov 14 15:29:40 2017 -0800

• fixup 11-way description refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html - lines changed 43, context: html, text, full: html, text

2bdca3d1d4f826e05bb597abee9508d4c50c69d0 Tue Nov 14 15:31:59 2017 -0800

• correct list of species in sGroup refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.11way.ra - lines changed 1, context: html, text, full: html, text

5023731f88ef52ef71aa8d37debc639d670e8a86 Tue Nov 14 15:33:35 2017 -0800

• correct shortLabel is Conservation refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.11way.ra - lines changed 1, context: html, text, full: html, text

88d645ebb17441000185bc5303ab1e332fea4bd7 Wed Nov 15 10:00:35 2017 -0800

• avoid gzip waiting for confirmation to overwrite refs #20479
  • src/hg/mouseStuff/chainToPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

1c0a252fc496333382df6b391646afca45b11d2f Thu Nov 16 14:08:47 2017 -0800

• eliminate confusion from new source version printout no redmine
  • src/utils/bedClip/tests/makefile - lines changed 6, context: html, text, full: html, text

ea289ea2ec73ce6da8c158fdb279e0f4b9881f96 Fri Nov 17 10:03:17 2017 -0800

• adding blatServers refs #18958 #17545 #18927
  • src/hg/makeDb/doc/colAng1/initialBuild.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/macNem1/initialBuild.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/rhiBie1/initialBuild.txt - lines changed 3, context: html, text, full: html, text

0e1c30edecf67391e0260ddee07c28b565bd5f44 Mon Nov 27 10:05:32 2017 -0800

• v358 final build refs #20479
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

cedef52b772e1cca44c8d8729289e50975506313 Mon Nov 27 10:06:16 2017 -0800

• New version number v358
  • 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