Commits for hiram

v344_base to v345_preview (2017-01-30 to 2017-02-06) v345

9d0dc96245478a27b3cb052677c4865e8f806dee Mon Jan 30 10:53:18 2017 -0800

• catch up documentation for micOch1 build refs #9871
  • src/hg/makeDb/doc/micOch1/initialBuild.txt - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/doc/micOch1/lastzRuns.txt - lines changed 78, context: html, text, full: html, text

d3526be1b8da33f949cced0dc28b411ee3e47b26 Mon Jan 30 10:55:19 2017 -0800

• setup gold table search rule refs #9871
  • src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra - lines changed 5, context: html, text, full: html, text

469444220a22cea814cb9e1d7cc29f36afad2ce3 Mon Jan 30 10:57:12 2017 -0800

• adding liftOver to bruMal2 no redmine
  • src/hg/makeDb/doc/bruMal1.txt - lines changed 17, context: html, text, full: html, text

0afe5f67095669bdf079ffe8f45538d6885ac83c Mon Jan 30 10:58:08 2017 -0800

• resetting common name no redmine
  • src/hg/makeDb/doc/caeSp111.txt - lines changed 7, context: html, text, full: html, text

b7c4b27d9f96045813713fda5ef129584bad9595 Mon Jan 30 11:02:44 2017 -0800

• document lastz/chain/net to rheMac2 no redmine
  • src/hg/makeDb/doc/chlSab2/lastzRuns.txt - lines changed 70, context: html, text, full: html, text

aca00cf8f71fe9ee4ce9bf2964c4da670c425873 Mon Jan 30 11:08:26 2017 -0800

• finish up lastz/chain/net runs for melGal5 to falPer1 and geoFor1 refs #18739
  • src/hg/makeDb/doc/galGal5/lastzRuns.txt - lines changed 17, context: html, text, full: html, text

576128c6c0a2f0d7702b72290d8d5b602bf1cf02 Mon Jan 30 11:09:32 2017 -0800

• reset default position to GULO refs #17180
  • src/hg/makeDb/doc/galVar1/initialBuild.txt - lines changed 8, context: html, text, full: html, text

e987c33b20c6b1450b6c0829aff2d16e19b9f19d Mon Jan 30 11:11:33 2017 -0800

• finish off patch9 refs #18274
  • src/hg/makeDb/doc/hg38/hg38Patch9.txt - lines changed 98, context: html, text, full: html, text

fefba1cf72903b09953370036f03347309df91e2 Mon Jan 30 11:11:51 2017 -0800

• finish off patch9 refs #18274
  • src/hg/makeDb/doc/hg38/patchDescr.pl - lines changed 3, context: html, text, full: html, text

f351dbb61024ffdccb21b52a40bc82970e8b39aa Mon Jan 30 11:43:43 2017 -0800

• fixup common name no redmine
  • src/hg/makeDb/doc/melHap1.txt - lines changed 5, context: html, text, full: html, text

c596180d1e3244635172a6623c89cff2c9bfdd82 Mon Jan 30 11:44:53 2017 -0800

• finish off melGal5/monDom5 lastz/chain/net refs #18739
  • src/hg/makeDb/doc/monDom5.txt - lines changed 4, context: html, text, full: html, text

1720e5b9586b7a4d269d0b667c6a5b2a81d55292 Mon Jan 30 11:46:11 2017 -0800

• liftOver to ornAna2 refs #15098
  • src/hg/makeDb/doc/ornAna1.txt - lines changed 15, context: html, text, full: html, text

59a5a56f6270ee6538bdaec401080a5409c722a5 Mon Jan 30 11:47:14 2017 -0800

• finish off taeGut2/melGal5 lastz/chain/net refs #18739
  • src/hg/makeDb/doc/taeGut2.txt - lines changed 1, context: html, text, full: html, text

ded3da06b9daa8f2367666ef901d181923d48f01 Mon Jan 30 13:51:07 2017 -0800

• script to work up composite chainNet trackDb from lists of species refs #18656
  • src/hg/makeDb/doc/rn6.txt - lines changed 47, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl - lines changed 164, context: html, text, full: html, text

009d40b43ba265c71c19062b3058f0f8aa1e34e3 Tue Jan 31 13:30:40 2017 -0800

• correct comments in 20 way headings refs #18656
  • src/hg/makeDb/doc/rn6.txt - lines changed 2, context: html, text, full: html, text

965dbf5fabf2bbf041fe65f449a475704e54067e Tue Jan 31 15:27:22 2017 -0800

• adding Curated and Predicted search rules for ncbiRefSeq refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 20, context: html, text, full: html, text

838df62dad1ec9e60a739a211277e5719c1e89c1 Wed Feb 1 15:53:24 2017 -0800

• Added colAng1 - Angolan colobus - Colobus angolensis palliatus - refs #17545
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text

afdcf49ed2769a475e844e0f6fe465ff53236686 Wed Feb 1 15:57:34 2017 -0800

• adding search rule for gold table refs #17545
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra - lines changed 5, context: html, text, full: html, text

7a77be9376f2f9c7829be5acb659eb32c6cbbd2b Wed Feb 1 16:11:46 2017 -0800

• fixup search rule for ncbiRefSeqMrna refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 10, context: html, text, full: html, text

e561b8edf9f16bd8067e68c7140a67bac6b765e7 Mon Feb 6 09:21:25 2017 -0800

• running up panTro4 and gorGor5 lastz runs refs #16036
  • src/hg/makeDb/doc/panPan2/lastzRuns.txt - lines changed 219, context: html, text, full: html, text