Commits for kate

v372_base to v373_preview (2018-10-01 to 2018-10-08) v373

8a75f8b98316f72a4539944c73e840126411a426 Thu Sep 13 12:49:04 2018 -0700

• Initial work for pack mode display of interactions as linked features. Doesn't recognize pack mode, and doesn't display as linked features (just as bed3). refs #21917
  • src/hg/hgTracks/bedTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/interactTrack.c - lines changed 25, context: html, text, full: html, text
  • src/hg/inc/interact.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 106, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text

8f7b62dddfdac702c0074c3d6b349182f1f14ec6 Mon Sep 17 10:19:19 2018 -0700

• Merge branch 'master' into interact-pack

442fef159db4b61a41789813c9068776ef2f8cfb Mon Sep 17 19:39:24 2018 -0700

• Pack mode. refs #21917
  • src/hg/hgTracks/bedTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/interactTrack.c - lines changed 77, context: html, text, full: html, text
  • src/hg/inc/interact.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 68, context: html, text, full: html, text

37af8b7789ebc58d6badf8d9ae2ccd3039adf940 Mon Sep 17 21:56:18 2018 -0700

• Pack mode display for interactions where source and target overlap, using thickStart/End. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/interact.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 56, context: html, text, full: html, text

6ee178c93b929d9ddd41d8647962a716c87fe7db Mon Sep 17 22:39:08 2018 -0700

• Forgive incorrect chromStart/chromEnd. And on click, find named items when pos doesn't do it. refs #21917
  • src/hg/hgc/interactClick.c - lines changed 37, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 2, context: html, text, full: html, text

35460385dc428f5357f9232a0e83547e955f8285 Mon Sep 17 22:39:57 2018 -0700

• Fix error.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.geneHancer.ra - lines changed 1, context: html, text, full: html, text

9ce15c632794253f032f387b7d2ee24b0a4cde97 Tue Sep 18 17:24:18 2018 -0700

• Add squish mode to linkedfeatures mode. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 1, context: html, text, full: html, text

cb385bfd125999cd75825332c08d4429e163de26 Thu Sep 20 13:12:22 2018 -0700

• Fixing geneHancer track config. refs #22048
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text

db44b993ec6123985aaae9aade94f329b0db49ec Sun Sep 23 21:03:19 2018 -0700

• Add option to merge interactions for a single target, in pack and squish modes. Initial version for demo. refs #21917
  • src/hg/hgTracks/hgTracks.h - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTracks/interactTrack.c - lines changed 69, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 19, context: html, text, full: html, text

38f76a98fd4df99ad172c8713df10546ba119f3d Sun Sep 23 21:23:09 2018 -0700

• In merged pack mode, distinguish target further by drawing in contrasting color (black if useColor on). refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 13, context: html, text, full: html, text

1c86690945dd3afba6ce4a0f5f6d0a44b9612220 Mon Sep 24 09:10:26 2018 -0700

• Remove barbs from merged interactions, as too confusing. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 4, context: html, text, full: html, text

39e533cc9ffcb46d9c484dc09a387a031a739391 Mon Sep 24 16:35:53 2018 -0700

• Updating from master
  • src/hg/hgTracks/interactTrack.c - lines changed 155, context: html, text, full: html, text
  • src/hg/inc/interact.h - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 193, context: html, text, full: html, text

46734f435d23f6919a08661b386c5a70a01a51cc Tue Sep 25 12:00:32 2018 -0700

• Add support for 'merged mode' track display. This mode merges directional interactions by source or target, and displays as linked features (not arcs). This was originally conceived by Max, and initially implemented as the pack mode for standard interaction display, but was extended as different track display in all modes so that arcs and linked features display can be viewed concurrently, By request of JK. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 277, context: html, text, full: html, text
  • src/hg/inc/interactUi.h - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 36, context: html, text, full: html, text
  • src/hg/lib/interactUi.c - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 29, context: html, text, full: html, text

0a037dc34719826e667970a3f7dc99140cc4eef6 Wed Sep 26 10:49:12 2018 -0700

• Fix pack mode on cross-chrom item. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 1, context: html, text, full: html, text

f5c2c152e1603b5657f7e11af28d1a8b85ba6a3d Wed Sep 26 11:27:46 2018 -0700

• Fix another problem with interchromosomal items in pack mode. refs #21917
  • src/hg/lib/interact.c - lines changed 17, context: html, text, full: html, text

cde6d1587f5f3b2f56de5c45125f42c24cfde4a3 Wed Sep 26 15:48:58 2018 -0700

• Support interchromosomal items in merge mode. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/interact.c - lines changed 1, context: html, text, full: html, text

6f1235bd145665106992ac47b99c383c2983a308 Wed Sep 26 15:51:42 2018 -0700

• Support interchromosomal items in merge mode. refs #21917
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

1626a52b02dcd43ea663946afc3f296a8ce9257b Wed Sep 26 16:38:26 2018 -0700

• Add click support to merged interactionss. refs #21917
  • src/hg/hgc/interactClick.c - lines changed 26, context: html, text, full: html, text

b87966ef79a5c54ed61f83bc59233f1628cd7ac7 Wed Sep 26 17:02:49 2018 -0700

• More click support for merged interactions. refs #21917
  • src/hg/hgc/interactClick.c - lines changed 17, context: html, text, full: html, text

2ea1942c2a0422e9ad0cda2e9ca6ae22232166bb Wed Sep 26 17:17:39 2018 -0700

• Switch dense mode display to linked-features style. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 1, context: html, text, full: html, text

229b9f6993152bab7202c2a32f461ecaa478e140 Mon Oct 1 16:28:22 2018 -0700

• Rename merge mode to cluster mode. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgc/interactClick.c - lines changed 14, context: html, text, full: html, text
  • src/hg/inc/interactUi.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/interactUi.c - lines changed 26, context: html, text, full: html, text

54e6ff68a081a4b6d7785d1329d48f67947e75bf Mon Oct 1 16:29:24 2018 -0700

• Rename merge mode to cluster mode. refs #21917
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 12, context: html, text, full: html, text

b40bfbe9e828a576e1f209923ec4100e92f2b133 Mon Oct 1 16:32:04 2018 -0700

• Fixing merge conflict.

d68dcad65fb5527d810d259e49891f764d954f14 Mon Oct 1 16:34:12 2018 -0700

• Merge branch 'interact-mergePack'

74f1973502355135843e87d38fec2019a0eaed73 Tue Oct 2 13:57:26 2018 -0700

• Fix defaults (set to DoubleElite subset). refs #22048
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 4, context: html, text, full: html, text

e8d73d075f5667438415ec1e549cd9df8efe499a Tue Oct 2 14:31:45 2018 -0700

• Fix details in cluster mode. refs #21917
  • src/hg/hgc/interactClick.c - lines changed 5, context: html, text, full: html, text

61981d22590032673103aa71408faa4842466dd8 Tue Oct 2 14:32:12 2018 -0700

• Add URL to cluster mode. refs #21917
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 2, context: html, text, full: html, text

03d59afaf32f77ee65773965da863711eda0d16c Tue Oct 2 16:22:47 2018 -0700

• Initial round of line-length and character encoding fixes to Simon's well-written description. refs #21917
  • src/hg/makeDb/trackDb/human/geneHancer.html - lines changed 51, context: html, text, full: html, text

7cea3bbd51d37d6b66c310d1e51ce0cc74ffd43e Tue Oct 2 16:24:04 2018 -0700

• Tweaking defaults. Clusters config likely not needing to be changed, so not leaving on default. refs #21917
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 1, context: html, text, full: html, text

ac6ca8a10b8e7e2c157f6ffbb41d0f269ce8737a Tue Oct 2 17:30:19 2018 -0700

• Formatting and some wordsmithing to conform to GB style. refs #21917
  • src/hg/makeDb/trackDb/human/geneHancer.html - lines changed 91, context: html, text, full: html, text

ddaf683e4f99f8b8173d4d045db1ba9222e3447c Tue Oct 2 18:26:49 2018 -0700

• Reorg to follow section conventions. refs #21917
  • src/hg/makeDb/trackDb/human/geneHancer.html - lines changed 93, context: html, text, full: html, text

e6bdae0038cce59383a30ab3ca1c199b43469694 Tue Oct 2 19:34:00 2018 -0700

• Polishing the track description. refs #21917
  • src/hg/makeDb/trackDb/human/geneHancer.html - lines changed 25, context: html, text, full: html, text

a42334fbd7b38aaa219821e02dc9eb5aeff64496 Thu Oct 4 11:54:56 2018 -0700

• Fix problem with click on 'feet', introduced with new cluster mode, and found by Jairo during QA. refs #21917
  • src/hg/hgc/interactClick.c - lines changed 4, context: html, text, full: html, text

efb0bb2e165326bbe6d8c71acd9d2e81cf0dc79a Thu Oct 4 14:55:00 2018 -0700

• Pack mode for non-directional interactions. And distingush source and target in packed mode with tall drawing. refs #21917
  • src/hg/hgTracks/interactTrack.c - lines changed 22, context: html, text, full: html, text

bc96093799bdac93cab20f88b245161d9c18bf76 Thu Oct 4 14:55:47 2018 -0700

• Merge branch 'interact-pack-short'