File Changes for hiram

v353_preview to v353_preview2 (2017-07-24 to 2017-07-31) v353

• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    9d5b06f905c0e52d661220bcf3815741cc0fb2e8 Wed Jul 26 16:17:39 2017 -0700
    eliminate duplicated ctTouchLastUse() call no redmine
• src/hg/makeDb/doc/mm10.txt
  • lines changed 178, context: html, text, full: html, text
    8ba05119d99c255424d8a1a2eed08bc5488814cc Mon Jul 31 10:07:53 2017 -0700
    add crispr.10K procedure and running up lastz for susScr11 and oreNil3 refs #19874 #19859 #19879
• src/hg/makeDb/doc/oreNil3/initialBuild.txt
  • lines changed 693, context: html, text, full: html, text
    e0d8b75b9c7c35528390d5c16141a1b94a8079f7 Sat Jul 29 10:27:20 2017 -0700
    ready for some pairWise alignments refs #19879
• src/hg/makeDb/doc/susScr11/initialBuild.txt
  • lines changed 708, context: html, text, full: html, text
    ca0f41c103a9bcfdf3be9c595ae17b7248f3d55e Tue Jul 25 14:51:11 2017 -0700
    running up repeatMasker for susScr11 refs #19859
  • lines changed 222, context: html, text, full: html, text
    edbdf249d5730d636f46b6fcfe3019988fc2280b Sat Jul 29 11:00:31 2017 -0700
    ready for pair-wise alignments refs #19859
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    a91fb9071ad6a67fb99e3e197bd6120a81051291 Sat Jul 29 09:54:57 2017 -0700
    Added oreNil3 - Nile tilapia refs #19879
  • lines changed 1, context: html, text, full: html, text
    eec976f8d7ec01f234e41a8b327e0309b0ecd9c1 Sat Jul 29 10:30:58 2017 -0700
    Added susScr11 - pig refs #19859
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    5d8b22f5b54930bec33cab3f81c8ddf8c33da8aa Thu Jul 27 20:46:47 2017 -0700
    Added susScr11; refs #19879
  • lines changed 1, context: html, text, full: html, text
    b5a3d8778deb037aecbbc698e4485faf957f1666 Thu Jul 27 20:48:54 2017 -0700
    Added susScr11; refs #19879
  • lines changed 17, context: html, text, full: html, text
    e25a611e1efa1976bcc0705a1d8b711bbd615f0f Thu Jul 27 20:57:51 2017 -0700
    Added oreNil3; refs #19879
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    a91fb9071ad6a67fb99e3e197bd6120a81051291 Sat Jul 29 09:54:57 2017 -0700
    Added oreNil3 - Nile tilapia refs #19879
  • lines changed 2, context: html, text, full: html, text
    eec976f8d7ec01f234e41a8b327e0309b0ecd9c1 Sat Jul 29 10:30:58 2017 -0700
    Added susScr11 - pig refs #19859
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    5d0f9197b76d7729cf53cb4a6b394fa842a15f51 Sat Jul 29 10:26:19 2017 -0700
    adding oreNil3 rules refs #19879
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
  • lines changed 1, context: html, text, full: html, text
    e4186ca1bb268888a0ea790c1b5286506955b5a0 Thu Jul 27 11:50:09 2017 -0700
    adding oreNil3 to the browser refs #19879
• src/hg/makeDb/trackDb/oreNil/oreNil3/description.html
  • lines changed 64, context: html, text, full: html, text
    e4186ca1bb268888a0ea790c1b5286506955b5a0 Thu Jul 27 11:50:09 2017 -0700
    adding oreNil3 to the browser refs #19879
• src/hg/makeDb/trackDb/oreNil/oreNil3/gap.html
  • lines changed 29, context: html, text, full: html, text
    e4186ca1bb268888a0ea790c1b5286506955b5a0 Thu Jul 27 11:50:09 2017 -0700
    adding oreNil3 to the browser refs #19879
• src/hg/makeDb/trackDb/oreNil/oreNil3/gold.html
  • lines changed 34, context: html, text, full: html, text
    e4186ca1bb268888a0ea790c1b5286506955b5a0 Thu Jul 27 11:50:09 2017 -0700
    adding oreNil3 to the browser refs #19879
• src/hg/makeDb/trackDb/oreNil/oreNil3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    e4186ca1bb268888a0ea790c1b5286506955b5a0 Thu Jul 27 11:50:09 2017 -0700
    adding oreNil3 to the browser refs #19879
  • lines changed 6, context: html, text, full: html, text
    f452aafd9d7c900070843984ac1f158b9da0c146 Sat Jul 29 10:02:44 2017 -0700
    Added gold table search rules refs #19879
• src/hg/makeDb/trackDb/pig/susScr11/description.html
  • lines changed 64, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
• src/hg/makeDb/trackDb/pig/susScr11/gap.html
  • lines changed 32, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
• src/hg/makeDb/trackDb/pig/susScr11/gold.html
  • lines changed 37, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
• src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
  • lines changed 5, context: html, text, full: html, text
    4c3b5c61f1201409474e58ad530969661246b177 Sat Jul 29 10:58:58 2017 -0700
    add gold table search rule refs #19859
• src/hg/mouseStuff/mafToFa/makefile
  • lines changed 14, context: html, text, full: html, text
    ebd0ff8090407946c1b4208f99dbdf519fed40e9 Tue Jul 25 22:38:09 2017 -0700
    modern makefile allows binary to build no redmine
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    eebd828cfa28186771c8ec257acc99f5cb467089 Tue Jul 25 11:21:39 2017 -0700
    adding susScr11 to the browser and fixup makeGenomeDb.pl to recognize new types of gaps refs #19859
• src/inc/common.mk
  • lines changed 8, context: html, text, full: html, text
    f04c258e3e27d16905684915df3ba0b611890f30 Wed Jul 26 10:29:41 2017 -0700
    fixup userApps build for Mac OSX build refs #19715
  • lines changed 9, context: html, text, full: html, text
    9ec5130a97fde5c6855b7d56f39c0d007aa5ff29 Wed Jul 26 10:57:42 2017 -0700
    rearrangement for Mac will not work on hgwdev refs #19715
• src/inc/userApp.mk
  • lines changed 2, context: html, text, full: html, text
    f04c258e3e27d16905684915df3ba0b611890f30 Wed Jul 26 10:29:41 2017 -0700
    fixup userApps build for Mac OSX build refs #19715
  • lines changed 2, context: html, text, full: html, text
    9ec5130a97fde5c6855b7d56f39c0d007aa5ff29 Wed Jul 26 10:57:42 2017 -0700
    rearrangement for Mac will not work on hgwdev refs #19715
• src/utils/crisprKmers/crisprKmers.c
  • lines changed 60, context: html, text, full: html, text
    8bd378fa491b953980381f804c91b6f240697d57 Mon Jul 24 10:00:51 2017 -0700
    change dumpKmers to dumpGuides and properly recognize only -NGG guides not the -NAG decoys refs #18969
  • lines changed 42, context: html, text, full: html, text
    0e23fd19b0162759909cee1861a70decad3e85f0 Tue Jul 25 22:04:10 2017 -0700
    marking duplicates during first queryVsSelf refs #18969
  • lines changed 6, context: html, text, full: html, text
    f6154dbb0025a2308f28e584a8cfacf1a68735bd Wed Jul 26 11:34:04 2017 -0700
    correct outage when endsAG was introduced as a filter during rangeScan refs #18969
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    d57b92e71287a64d310eea3185b3642cd33e4751 Mon Jul 31 10:22:59 2017 -0700
    v353 preview2 refs #19846