Commits for kate

v388_preview to v388_preview2 (2019-09-09 to 2019-09-16) v388

c1e0d2307cfe3e7c75cfd54ae8626a797d5b7adb Sun Jul 28 20:20:04 2019 -0700

• Enhancer/gene interact track. refs #23881
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 9, context: html, text, full: html, text

2b0cfc0601b90ae87096a86a401e5117f24b58b6 Tue Jul 30 11:49:08 2019 -0700

• Merge branch 'master' into mouseInteract

75f11715852d9fc54c7f0eb6b7a12665d913fd7e Wed Jul 31 16:43:00 2019 -0700

• Track config for mouse enhancer/gene track from Ren lab + EPDNew. refs #23881
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 5, context: html, text, full: html, text

52f070230fc74d3e6b45fc5ac13d4a8b051d7b0a Tue Aug 6 15:48:19 2019 -0700

• Expand to two datasets (all and replicated), following pattern of GeneHancer. refs #23881
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra - lines changed 83, context: html, text, full: html, text

172d7a0e89e4ad6b243adad0fc6c5b97abd93052 Tue Aug 6 16:28:07 2019 -0700

• Add track description. refs #23881
  • src/hg/makeDb/trackDb/mouse/mm10/enhancerGeneInteract.html - lines changed 50, context: html, text, full: html, text

0704d60df5fb8dca2aacab2a553477397bb26af1 Wed Aug 7 16:42:47 2019 -0700

• Add ATAC-seq track, tune up track config for related tracks. refs #23970
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra - lines changed 1221, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.chromHmm.ra - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra - lines changed 18, context: html, text, full: html, text

b48c2ab7665ace5fbbb62dd8496a759f7533bf02 Mon Aug 12 09:10:09 2019 -0700

• Swap short label orders to match other tracks. refs #23693
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra - lines changed 1127, context: html, text, full: html, text

a117c07ee74b6916d4e1d52757a8d874e0ad78f8 Fri Aug 23 10:14:01 2019 -0700

• Merge branch 'master' into mouseInteract

f03adc9de6991986db1c1f611f81eac25cc06604 Mon Sep 9 13:25:26 2019 -0700

• Merge branch 'master' into mouseInteract

8d264f60e756c0949a00e443988305e45ea1d695 Mon Sep 9 15:19:41 2019 -0700

• Use pooled bed files (update from Ren lab). refs #23970
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra - lines changed 69, context: html, text, full: html, text

52415ddd22b076a8da4d20f36fa5bd417eec9a92 Mon Sep 9 15:24:45 2019 -0700

• Remove superfluous lines. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra - lines changed 65, context: html, text, full: html, text

d13cfad020fadc5a52eaa649b048308f593da89e Mon Sep 9 15:28:04 2019 -0700

• Cleanup. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra - lines changed 66, context: html, text, full: html, text

280b6ce6b208cdb9a6c78f22de7eca58ac9d7710 Wed Sep 11 10:27:22 2019 -0700

• Clarification on long labels. refs #23693
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra - lines changed 144, context: html, text, full: html, text

601ece4d47e590855e1232bc968593299fc4b703 Wed Sep 11 11:09:09 2019 -0700

• Clean up and expand interactMultiRegion trackDb seetting to specify padding. Needed for transEqtl (huge and chross-chrom interactions). refs #24037
  • src/hg/hgc/interactClick.c - lines changed 21, context: html, text, full: html, text

e4a5730f471d61aed02989f57e9dfe1fea275c68 Wed Sep 11 13:09:55 2019 -0700

• Merge branch 'master' into mouseEncode

cd91480db30f283eddedba67051be27b6522ec15 Wed Sep 11 14:40:34 2019 -0700

• Refine long labels. refs #23693
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.ra - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/enhancerGeneInteract.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.enhancerGeneInteract.ra - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra - lines changed 1129, context: html, text, full: html, text

5968091eaab76ed5b489b355fb9e98d70fd2d3f2 Wed Sep 11 14:51:25 2019 -0700

• Cleanup ra files, add html. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra - lines changed 1091, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 477, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra - lines changed 11296, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3Reg.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.atac.ra - lines changed 1091, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.chromHmm.ra - lines changed 477, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra - lines changed 11296, context: html, text, full: html, text

da82c8df231e66625b605ff7dac241d47d3ee0dc Wed Sep 11 14:55:02 2019 -0700

• Replace offending dots in track names from Ren lab hub. refs #23693
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra - lines changed 1126, context: html, text, full: html, text

fb30d552b09686ac1f7d26d10ea821c0e3a0f821 Wed Sep 11 14:56:49 2019 -0700

• Correct P0 long labels. refs #23970
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra - lines changed 18, context: html, text, full: html, text

1b9178e6f9a4093b47848db5d037a704c7352749 Wed Sep 11 15:01:09 2019 -0700

• Correct P0 long labels. refs #24128
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 9, context: html, text, full: html, text

0ad9db5d262850c4b159bad0eb9831ddd1e97cbb Wed Sep 11 15:11:54 2019 -0700

• Fix link. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/encode3Reg.html - lines changed 1, context: html, text, full: html, text

70eb0c6ecc1ae9d8cc66c1bc59e477ac1eb91d9f Wed Sep 11 15:18:19 2019 -0700

• Add link. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/encode3Reg.html - lines changed 1, context: html, text, full: html, text

5f8bd704e0605123dfdd32087d8fd70f74091676 Wed Sep 11 15:19:20 2019 -0700

• Minor label relabeling and file renaming. refs #23880
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra - lines changed 133, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

a7926f9fedb679fc0a1fade0c4f21311d7f32dc6 Wed Sep 11 15:28:18 2019 -0700

• Trim shortlabels. refs #24128
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 15, context: html, text, full: html, text

5b98413917254114a1219389ec8b9ee0668df170 Wed Sep 11 16:43:50 2019 -0700

• Tweak default on tracks. refs #23990
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra - lines changed 173, context: html, text, full: html, text

ecdc82eb342c99c36ac63c963cd2261003595a0f Wed Sep 11 16:44:37 2019 -0700

• Tweak default on tracks. refs #23990
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 1, context: html, text, full: html, text

9a754a05249437c33171743db07a02ab6653ebb9 Wed Sep 11 16:45:17 2019 -0700

• Merge branch 'mouseEncode'

36cb847f6b7291b1cb47fa503dbfd3c9beca741d Wed Sep 11 17:10:11 2019 -0700

• Fix up filename problem. refs #23881
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.ra - lines changed 29, context: html, text, full: html, text

f6e23d1d07c38b1a7cefd03393ec92856d5bb71c Thu Sep 12 12:42:57 2019 -0700

• Polish track description. refs #24128
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html - lines changed 70, context: html, text, full: html, text

af461ddaef211c16a3ca52913df3f4c9a95ed48d Thu Sep 12 13:38:55 2019 -0700

• Extend labelOnFeature setting to support dense mode w/o labels (as usual in our tracks). Using this feature in chromatin state tracks. refs #24128
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html - lines changed 5, context: html, text, full: html, text

2876cdada90cb8d845ab0b06cec817f83346400a Thu Sep 12 13:59:17 2019 -0700

• Add color patches to track description. refs #23693
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenAtac.html - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenHistone.html - lines changed 8, context: html, text, full: html, text

fe51985b7657e446612d290edc989d5861a4fa4e Fri Sep 13 09:33:52 2019 -0700

• Remove DOS line ends.
  • src/hg/makeDb/trackDb/mouse/mm10/encode3RenAtac.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)