Commits for hiram

v351_base to v352_preview (2017-06-26 to 2017-07-03) v352

b88aaef8cd105d1fed104c90036c6dddf610da7c Fri Jun 30 09:11:47 2017 -0700

• updated with editorial suggestions refs #19704
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 4, context: html, text, full: html, text

dfa68297f49c4d765765d9a91b368a21c12edefc Fri Jun 30 10:35:52 2017 -0700

• updated with editorial suggestions refs #19704
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 9, context: html, text, full: html, text

bde35017674c354a9c3b455bd284df54e16c148b Fri Jun 30 10:45:08 2017 -0700

• remove bogus </I> tag on Bio* ID; info lines refs #19704
  • src/hg/makeDb/trackDb/bonobo/panPan2/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro5/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droSim2/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor5/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macNem1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/description.html - lines changed 2, context: html, text, full: html, text

b9caf1770bd8154dd80f5596c9f2d0fc494de3ea Fri Jun 30 13:52:28 2017 -0700

• adding in mouse strain hub reference refs #13553
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 1, context: html, text, full: html, text

372f1fef9075019ab06e62e178f7d2df989d0cbd Fri Jun 30 17:19:06 2017 -0700

• working up brute force crispr scoring scheme refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 235, context: html, text, full: html, text
  • src/utils/crisprKmers/makefile - lines changed 3, context: html, text, full: html, text

48d09ab3cbb4ce1bb172e0479f1e80f878dac655 Sat Jul 1 00:16:53 2017 -0700

• this is getting close refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 153, context: html, text, full: html, text

7a9f95730b58e1d2eb3fc8dd33c72d9b9c8f07cd Mon Jul 3 10:02:41 2017 -0700

• this is not fast enough for crispr off target calculation it can only do one in 8 seconds or 39 million comparisons per second on hg38 but it can find the crisprs rapidly 85 seconds for hg38 scan over 300 million crisprs at 3.7 million per second refs #18969
  • src/utils/crisprKmers/crisprKmers.c - lines changed 91, context: html, text, full: html, text

3ce9ba8ad4f1e34411e3e4d13a4fa8e5a8c00574 Mon Jul 3 10:04:49 2017 -0700

• adding papAnu3 lastz chainNet refs #19660
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 61, context: html, text, full: html, text

b9ccb5fbc99dc33e5a3035a09eafcdab754eac4e Mon Jul 3 10:05:55 2017 -0700

• adding 185-way multiz refs #19533
  • src/hg/makeDb/trackDb/HBV/hbv1/trackDb.185way.ra - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/HBV/hbv1/trackDb.ra - lines changed 2, context: html, text, full: html, text

e6f9bb72c960f75055cb33cb4fff01baebe1eb0b Mon Jul 3 10:06:47 2017 -0700

• correctly using tmp directories for large sets of files refs #19514
  • src/hg/utils/automation/doCrispr.pl - lines changed 6, context: html, text, full: html, text

5a306a209a18b2306b421425cf3d61ad8a96b7af Mon Jul 3 10:07:29 2017 -0700

• FTP server at Ensembl has changed refs #19526
  • src/hg/utils/automation/findEnsFtpNames.sh - lines changed 23, context: html, text, full: html, text

18cf4bfa9b4687d0a3aad5aa04fa889843ee757a Mon Jul 3 10:25:21 2017 -0700

• v351 final build refs #19715
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text