Commits for hiram

v349_preview2 to v349_base (2017-05-08 to 2017-05-15) v349

84dba5bd375f9fe037ae695886b6ca82ce5cceb6 Mon May 8 10:24:36 2017 -0700

• adding chrPic2 rules and eliminate duplicate check for chainId refs #13166
  • src/hg/makeDb/schema/all.joiner - lines changed 13, context: html, text, full: html, text

a78ec0caef7d1fb397793f347bf6a5fb581de2bf Mon May 8 13:18:10 2017 -0700

• the chainId rule needs to be there causes duplicate checks refs #13166
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text

1dbb921507c9f41988f5b9a8f806eddeca1de6e0 Tue May 9 10:48:54 2017 -0700

• recognize hgComposite trash files and no need to read files to touch them refs #11630
  • src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c - lines changed 14, context: html, text, full: html, text

9696526fdb03bf1abb90a0c6a91db36b0181db36 Tue May 9 11:19:33 2017 -0700

• adding blat servers refs #16628
  • src/hg/makeDb/doc/ci3/initialBuild.txt - lines changed 120, context: html, text, full: html, text

a5f55498675912016c945acd791be4128341f350 Tue May 9 13:48:25 2017 -0700

• imported script from the git hub refs #18968
  • src/hg/makeDb/crisprTrack/crisprAddGenome.py - lines changed 561, context: html, text, full: html, text

dcd8fb5432eb66de1dcfe8de0486153cfeb63025 Tue May 9 14:50:45 2017 -0700

• there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
  • src/utils/qa/weeklybld/doHgNearTestRobot.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doHgTablesTestRobot.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doLiftOverTestRobot.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview2.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doTrackCheckRobot.csh - lines changed 2, context: html, text, full: html, text

1044a6388a242b7007db966548bd8fc3e713407b Tue May 9 14:53:33 2017 -0700

• there is no email address for USER@soe.ucsc.edu so eliminate that from mail commands no redmine
  • src/utils/qa/weeklybld/makeStrictBeta.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/moveBranchTag.csh - lines changed 1, context: html, text, full: html, text

b6a22c9242b039dc11b4e30378dfbad356f0edf5 Tue May 9 15:26:40 2017 -0700

• adding blat servers refs #15096
  • src/hg/makeDb/doc/aquChr2/initialBuild.txt - lines changed 12, context: html, text, full: html, text

a3d4d044a2c0d48a13792ba44b781439b64dec6a Wed May 10 11:27:12 2017 -0700

• from: NIH National Cancer Institute via https://commons.wikimedia.org/wiki/File:Papilloma_virus_(hpv).jpg refs #18971
  • src/hg/htdocs/images/hpv1.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

8f070a0b99b2a397d2be0215198089930272cf6f Wed May 10 11:39:13 2017 -0700

• eliminate bogus </I> tag refs #18971
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 2, context: html, text, full: html, text

67dc46bec08d36858fd06f48a6c8735812e2c44d Wed May 10 11:41:04 2017 -0700

• initial files from makeGenomeDb.pl refs #18971
  • src/hg/makeDb/trackDb/HPV/hpv1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/HPV/hpv1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/HPV/hpv1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/HPV/hpv1/trackDb.ra - lines changed 8, context: html, text, full: html, text

a76c2ddec0804734fc3c2cfa1bce1b567456a2e0 Wed May 10 13:17:45 2017 -0700

• add gold search rule refs #18971
  • src/hg/makeDb/trackDb/HPV/hpv1/trackDb.ra - lines changed 5, context: html, text, full: html, text

3a340242689d5e3c1843c38a897f147f68e6fb72 Wed May 10 16:31:19 2017 -0700

• done with masking refs #18971
  • src/hg/makeDb/doc/hpv1/initialBuild.txt - lines changed 729, context: html, text, full: html, text

88b767d53c72fb363d33b118dfe46cbe6450c931 Wed May 10 18:34:17 2017 -0700

• adding hpv1 Human papillomavirus type 90 - refs #18971
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

0334129bbf3460f87cde95e8e25eedcf7f440e22 Fri May 12 08:20:51 2017 -0700

• genbank loaded nothing ? refs #18971
  • src/hg/makeDb/doc/hpv1/initialBuild.txt - lines changed 212, context: html, text, full: html, text

9c6973bc64e6f6d22bfe1d6afe5dec4f81fe4c2b Fri May 12 08:24:53 2017 -0700

• panTro5 hg19 chainNet per user request refs #19343
  • src/hg/makeDb/doc/hg19.txt - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro5/lastzRuns.txt - lines changed 23, context: html, text, full: html, text

0aadfe099a9b23771fb238be21aa8c31bb82cf9a Fri May 12 09:22:09 2017 -0700

• changing blastz to lastz on README references refs #19343
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 9, context: html, text, full: html, text

3fd1fd8a1a68b38acdaad9ce8c44048d44ac06d8 Fri May 12 09:29:36 2017 -0700

• new default position recommendation from regeneron refs #19228
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 3, context: html, text, full: html, text

1f0b027a3b27bb19bbf97cc3381e17e1ca4be6b2 Fri May 12 09:51:53 2017 -0700

• reset default visibilities on recommendation from Regeneron refs #19228
  • src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 19, context: html, text, full: html, text

17d8c4c98bf3668bf19c8562ca36f11522e3ed32 Fri May 12 10:30:59 2017 -0700

• new default position from Regeneron recommendation refs #19228
  • src/hg/makeDb/doc/criGri1.txt - lines changed 5, context: html, text, full: html, text

4b807dd1a1bde4abc5c02e3788aeadce8fc9e81d Sun May 14 22:07:01 2017 -0700

• 47-way diagram for HPV1 refs #18971
  • src/hg/htdocs/images/phylo/hpv1_47way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

863b311f26403a3d457d75a732d8c69a55bb4bbb Mon May 15 09:58:18 2017 -0700

• v349 final build refs #19342
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

ba9d5d0321eac8766a88194623cbd51b46b34d0d Mon May 15 09:59:09 2017 -0700

• New version number v349
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text