Commits for hiram

v357_preview2 to v357_base (2017-10-23 to 2017-10-30) v357

94d765a1126e6bf7f1f5bbfa8b1fae7dfc5e7965 Mon Oct 23 13:53:33 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text

5ebe8e073583b447d578d1c92436fa19dae070d2 Mon Oct 23 13:54:39 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/human/chainNetLegacy.ra - lines changed 15, context: html, text, full: html, text

5a204646f2a4a6e1e45bfc0e87a6c4953b2252ec Mon Oct 23 13:56:38 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/human/hg38/cons27way.html - lines changed 459, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.27way.ra - lines changed 104, context: html, text, full: html, text

4fdfdaf637c86ded702ea684187d9608364eaf25 Mon Oct 23 13:59:48 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 491, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

4de281573b25b449fc527b7af5ae6d286c98fda9 Tue Oct 24 07:17:15 2017 -0700

• release tag needs to be is sub-stanzas fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text

fb093188e27adfbac846c6659421449be6be79b7 Tue Oct 24 07:47:06 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text

679c983dac3ede4d8d57f13fdd49bc7d0117111f Tue Oct 24 07:53:16 2017 -0700

• fixing up chainNet composites on hg38 and mm10 refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 16, context: html, text, full: html, text

7d2f9adebad1e5e6a47f3fcd8f6e5354f5e7b333 Tue Oct 24 10:29:41 2017 -0700

• chainMicMur1 here causes difficlty refs #20216
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text

4f73a4036b497b359ff20d1396bddc0cbfa6e800 Tue Oct 24 12:11:21 2017 -0700

• correct name of this composite track refs #200216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 1, context: html, text, full: html, text

e42a11b8bd0471b5856be5275c9e249786dec8df Tue Oct 24 12:49:00 2017 -0700

• composite track is referenced in the sub-tracks, correct name everywhere refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 78, context: html, text, full: html, text

5ea9901fe8b5eb2a58fbf03512f43af63f3d3893 Wed Oct 25 10:17:04 2017 -0700

• update ensGeneDb list to new assemblies refs #20304
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text

a89bf4ec9c46b355183eaa5901a8d01dd3b0c5d5 Wed Oct 25 11:37:26 2017 -0700

• make note that customFactoryTestExistence() in customFactory.c is depending upon the ctTouchLastUse() function here no redmine
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text

52c52b7de3078ef92d4126ebbc8fa0fbd4a7d8b2 Wed Oct 25 12:59:21 2017 -0700

• run up liftOvers between danRer10 and danRer11 refs #19459
  • src/hg/makeDb/doc/danRer10/initialBuild.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer11/initialBuild.txt - lines changed 7, context: html, text, full: html, text

88baafd974185837bf265f2b774d86300ab4c039 Thu Oct 26 06:36:53 2017 -0700

• spelling correction, no redmine
  • src/lib/font/README - lines changed 2, context: html, text, full: html, text

6d4605b31566016f6679d888799edb6efe8595ec Thu Oct 26 14:53:51 2017 -0700

• fixup the list for notEnsemblTranscriptId to remove dbs with ensGene tracks refs #20393
  • src/hg/makeDb/schema/all.joiner - lines changed 7, context: html, text, full: html, text

7964fdd5f6bc230448d412e7ff90e72a5a0be327 Fri Oct 27 11:00:43 2017 -0700

• working up syntenic and recip best chainNet composites refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra - lines changed 530, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra - lines changed 562, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 13, context: html, text, full: html, text

01944b512a611e4336f5ebcb8cd01d302f86cabc Fri Oct 27 11:02:44 2017 -0700

• expand to allow syntenic and recipBest composites refs #20216
  • src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl - lines changed 34, context: html, text, full: html, text

8e61a32fe3e5f32981c141fe50c938e8edf36a8e Fri Oct 27 11:07:00 2017 -0700

• extend to allow loading of recip best chainNet tables refs #20216
  • src/hg/utils/automation/doRecipBest.pl - lines changed 58, context: html, text, full: html, text

4fb8f36b7355d5125677ed33d6f37e92d0cdc0d5 Fri Oct 27 13:50:37 2017 -0700

• loading up the recip best chainNet tracks for primate alignments refs #20216
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 192, context: html, text, full: html, text
  • src/hg/makeDb/doc/tarSyr2/lastzRuns.txt - lines changed 6, context: html, text, full: html, text

80da8468b99e8aa5b321596d767e2bbe7fd78314 Fri Oct 27 14:06:11 2017 -0700

• correct command line refs #19154
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 1, context: html, text, full: html, text

5c98f02d8d0dabe2cec8ab305b6dee180b1595d5 Sat Oct 28 10:17:11 2017 -0700

• better short labels refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra - lines changed 194, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra - lines changed 214, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 24, context: html, text, full: html, text

0ea5983d4c7361a905b2a050bb41ed784cd1de27 Sat Oct 28 10:22:38 2017 -0700

• working up syntenic and recip best chainNet composites refs #20216
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text

3dc66b70ef8c94aa79a6f64e50ba6cb598aee4aa Mon Oct 30 10:00:33 2017 -0700

• catching up with loading recip best and syntenic net chainNet tracks refs #20216
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 413, context: html, text, full: html, text

b70bcbcb35470784e3f675c5292cbda4f3ee1d6c Mon Oct 30 10:21:12 2017 -0700

• v357 final build refs #20358
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

ee250cad347b57996f7cc1125d4be37f49c7fd06 Mon Oct 30 10:22:04 2017 -0700

• New version number v357
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text