Commits for hiram

v349_base to v350_preview (2017-05-15 to 2017-05-22) v350

c63be670d36d15c7b2d0ee04e04b38bfb49af222 Tue May 16 11:00:25 2017 -0700

• allow xenoRefGene table to be used refs #18969
  • src/utils/doLocusName - lines changed 2, context: html, text, full: html, text

0645c47bfe34098da9797bc094067b54b93fd20b Tue May 16 16:12:38 2017 -0700

• completed xenLae2 recip best refs #19151
  • src/hg/makeDb/doc/xenTro9/lastzRuns.txt - lines changed 7, context: html, text, full: html, text

be3cc3e70a0b4b4d7cd81b495e2d8d9e3ecae43d Wed May 17 09:07:23 2017 -0700

• the tupChi1 4-way track is alpha only refs #19403
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

862daf89620592b91269007bc40b9ae536c64969 Thu May 18 10:06:21 2017 -0700

• correctly recognize _ in unlocalized scaffold names for galGal5 refs #17168
  • src/hg/utils/automation/ucscToINSDC.sh - lines changed 1, context: html, text, full: html, text

d7e3ab057c8bf9de5ec33caece2535b677cd0336 Thu May 18 10:07:41 2017 -0700

• correctly update md5sum.txt file for galGal5 refs #17168
  • src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 5, context: html, text, full: html, text

d7ae1e8d7f7a1963cd8ce324d8e0abc1710b95d1 Thu May 18 10:10:01 2017 -0700

• allow photo to not exist refs #13553
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 15, context: html, text, full: html, text

fb7941b38b26040f9c23eaa4578f68c8e496d110 Thu May 18 10:10:50 2017 -0700

• adding the gapOverlap track procedure refs #13553
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 20, context: html, text, full: html, text

3c458131ec75bac1713f5baa720624255f6f9b22 Thu May 18 10:39:52 2017 -0700

• updating anaPla apaSpi geoFor and zonAlb no redmine
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

fb7b1d70a75733623f25f4c276897b4f2089005d Thu May 18 10:40:56 2017 -0700

• adding 195way rules no redmine
  • src/hg/utils/phyloTrees/makefile - lines changed 10, context: html, text, full: html, text

69b103ed65e09747f59b59e8cca624ef68976b0d Thu May 18 10:41:58 2017 -0700

• adding gekJap1, proMuc1, thaSir1, xenLae2, xenTro9 no redmine
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 6, context: html, text, full: html, text

c8623d4f6f811ad58339d934f1d37142ab5ba9d9 Thu May 18 10:42:55 2017 -0700

• adding comment about key for hash no redmine
  • src/hg/utils/phyloTrees/worms26way.chainNet.pl - lines changed 1, context: html, text, full: html, text

899b390be2ea230d0372dcb5f3ac9ab8d36f933c Thu May 18 10:45:58 2017 -0700

• catching up a few stray tracks to prepare for release refs #13166
  • src/hg/makeDb/doc/chrPic2.txt - lines changed 210, context: html, text, full: html, text

96f7d63e0f50c7bdce4072e4b4bb91efd435f57a Thu May 18 10:50:05 2017 -0700

• liftOver to micMur3 refs #18984
  • src/hg/makeDb/doc/micMur1.txt - lines changed 14, context: html, text, full: html, text

d59c89099d4cb7380e79d27c480b38249011c00a Thu May 18 10:54:31 2017 -0700

• liftOver to micMur3 refs #18984
  • src/hg/makeDb/doc/micMur2/initialBuild.txt - lines changed 36, context: html, text, full: html, text

f3671e97ff62b9133727a4d32093c7dd6882d2d2 Thu May 18 11:01:03 2017 -0700

• adding chainNet/lastz mm10 criGri1 to catch up criGri1 with standard lastz/chainNet refs #19228
  • src/hg/makeDb/doc/criGri1.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 57, context: html, text, full: html, text

a9b8b1f4f61861850714790a26097dfcf1d49a7e Thu May 18 11:04:57 2017 -0700

• adding assembly info comment data from NCBI references refs #15056
  • src/hg/makeDb/doc/nanPar1/initialBuild.txt - lines changed 29, context: html, text, full: html, text

47440f5d8fba85a17d4afed0df71f37db01f6678 Thu May 18 11:06:15 2017 -0700

• catching up outstanding procedures refs #16535
  • src/hg/makeDb/doc/oxyTri2/initialBuild.txt - lines changed 151, context: html, text, full: html, text

ea5d2b90084ece5ead31bb8627b08097ce77c656 Thu May 18 11:10:46 2017 -0700

• catching up build procedures, no redmine
  • src/hg/makeDb/doc/worms/ancCey1.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/worms/burXyl1.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/caeAng2.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/worms/caeSp51.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/worms/dirImm1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/melInc2.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/necAme1.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/priExs1.txt - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/priPac3.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/worms/strRat1.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/worms/strRat2.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/triSpi1.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/triSui1.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

cc4f3f178daaf46cf06567a6f29ee0b4e261dd71 Thu May 18 11:12:43 2017 -0700

• running makePushQ with the redmine listings refs #19151
  • src/hg/makeDb/doc/xenLae2/initialBuild.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro9/initialBuild.txt - lines changed 3, context: html, text, full: html, text

4d348026d7eace69ca5e25c2a3da5f07672fb268 Thu May 18 11:15:10 2017 -0700

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

81765a9713ec8020330790a0fb445431de0afc9f Thu May 18 11:16:31 2017 -0700

• adding gold search rules refs #18984
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra - lines changed 5, context: html, text, full: html, text

a5baef17b79d806a60d886cec056f0991a4eee14 Thu May 18 11:30:12 2017 -0700

• add noSequenceVerify option to speed up procedure refs #13673
  • src/utils/bamToPsl/bamToPsl.c - lines changed 13, context: html, text, full: html, text

56da8a5745b1ef79c8087ab53e3590e4395d0751 Thu May 18 11:34:20 2017 -0700

• catch up checkin no redmine
  • src/utils/ncbi/createNcbiCytoBand.pl - lines changed 1, context: html, text, full: html, text
  • src/utils/ncbi/cytoBandVerify.pl - lines changed 3, context: html, text, full: html, text

b0879b9b7a1fffb44a187b7c56507ab862cf581b Thu May 18 11:37:03 2017 -0700

• update Crowned_crain and Houbara_bustard no redmine
  • src/hg/utils/phyloTrees/191way.commonNames.nh - lines changed 2, context: html, text, full: html, text

a694e0a184fd207b5ca389e1b8697e5564b000a0 Thu May 18 22:31:55 2017 -0700

• adding tandem dup procedure refs #13553
  • src/hg/utils/automation/doTandemDup.pl - lines changed 392, context: html, text, full: html, text
  • src/hg/utils/automation/kmerCollapsePairedEnds.pl - lines changed 87, context: html, text, full: html, text
  • src/hg/utils/automation/kmerPairs.pl - lines changed 71, context: html, text, full: html, text
  • src/hg/utils/automation/kmerPrint.pl - lines changed 69, context: html, text, full: html, text

656a844ac6599a72350c4dbd6087eae57fb8a2a1 Fri May 19 15:01:00 2017 -0700

• allow collapsePairedEnds to have a min size so it can filter the final output much faster and correctly build bb file so it will display properly refs #13553
  • src/hg/utils/automation/doTandemDup.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/kmerCollapsePairedEnds.pl - lines changed 6, context: html, text, full: html, text

f8ee6d9dbaee339e156b691e8e6ffcc526e49ccd Fri May 19 15:35:33 2017 -0700

• remove debug printf refs #13553
  • src/hg/utils/automation/doTandemDup.pl - lines changed 1, context: html, text, full: html, text

e9481e0572648a23ef83542618bb67bbff3ad3e8 Mon May 22 10:02:55 2017 -0700

• v350 preview1 refs #19342
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text