Commits for hiram

v344_preview2 to v344_base (2017-01-23 to 2017-01-30) v344

7b753b9d978b16b5aa3bdbbc6e30ca8ee09d0423 Tue Jan 24 08:06:17 2017 -0800

• catching up chain net overrides for rat rn6 and 20-way alignment refs #18656
  • src/hg/makeDb/trackDb/bats/rouAeg1/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bison/bisBis1/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.20way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra - lines changed 5, context: html, text, full: html, text

937738d7b80e53631d5598a2731aac63c54430fe Tue Jan 24 10:59:33 2017 -0800

• description page for 20-way refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/cons20way.html - lines changed 465, context: html, text, full: html, text

a9d6033117bea69474ef6c633381794d8fe76a74 Tue Jan 24 11:15:31 2017 -0800

• reset MAF type used in alignment refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/cons20way.html - lines changed 20, context: html, text, full: html, text

20459ec6f898bc8b5afeddb582b249cf007a185b Tue Jan 24 15:21:48 2017 -0800

• completed 20-way alignment refs #18656
  • src/hg/makeDb/doc/rn6.txt - lines changed 1650, context: html, text, full: html, text

3871f1bd6012e5fc02fb67ff508ffaf560e129ec Wed Jan 25 09:29:47 2017 -0800

• photo of prairie mole from National Park Service refs #9871
  • src/hg/htdocs/images/Microtus_ochrogaster.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

4af6dcf3c8c13804bb4d4a52587985345f99714e Wed Jan 25 10:25:03 2017 -0800

• trackDb files for micOch1 refs #9871
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra - lines changed 8, context: html, text, full: html, text

f204420da68ebeb775d15a9668329833d59aeafd Wed Jan 25 13:07:56 2017 -0800

• correct viewLimits on the phyloP track refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.20way.ra - lines changed 2, context: html, text, full: html, text

3648c849e58893972d8c79310950ec54ce1a854e Wed Jan 25 19:52:16 2017 -0800

• Added micOch1 Microtus ochrogaster - prairie vole refs #9871
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

c95e40873d16d2480733c98f7752ca4b26d3a8e6 Thu Jan 26 11:00:47 2017 -0800

• adding micOch1 to the update alignments refs #9871
  • 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

ca8aad823e63a1a4b3aca4739d054f9232562b0b Thu Jan 26 11:01:51 2017 -0800

• build doc for micOch1 refs #9871
  • src/hg/makeDb/doc/micOch1/initialBuild.txt - lines changed 703, context: html, text, full: html, text
  • src/hg/makeDb/doc/micOch1/ucscCompositeAgp.pl - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/micOch1/unlocalized.pl - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/micOch1/unplaced.pl - lines changed 34, context: html, text, full: html, text

7fd8cdb277f61ae6edc8cc5261bf8068d20a9de9 Thu Jan 26 12:23:19 2017 -0800

• adding rules for micOch1 refs #9871
  • src/hg/makeDb/schema/all.joiner - lines changed 14, context: html, text, full: html, text

910444b42b5afa38484b578483d46da3b3ac1bf7 Sat Jan 28 08:32:32 2017 -0800

• turning on composite chain/net tracks and 20-way alignment refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.20way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/vertebrateChainNet.ra - lines changed 338, context: html, text, full: html, text

1409339509c798dd049a8c99a61881413fedcf88 Sun Jan 29 13:30:25 2017 -0800

• add documentation for chain net composite and reset primate label to primates refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html - lines changed 164, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/vertebrateChainNet.ra - lines changed 1, context: html, text, full: html, text

77b3694f04fb7a5010a04c1b57c518cac46368c3 Mon Jan 30 09:15:51 2017 -0800

• catch up geoFor1 and falPer1 lastz/chain/net refs #18739
  • src/hg/makeDb/doc/melGal5/initialBuild.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/melGal5/lastzRuns.txt - lines changed 119, context: html, text, full: html, text

fc49d9c94c69d3c19ecff8a7a7598f2c4630445e Mon Jan 30 10:01:14 2017 -0800

• v344 final build refs #18686
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

aab9cab184eb26a03a49ef5cf63cc8a503972a85 Mon Jan 30 10:02:09 2017 -0800

• New version number v344
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text