File Changes for kate

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

• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    442fef159db4b61a41789813c9068776ef2f8cfb Mon Sep 17 19:39:24 2018 -0700
    Pack mode. refs #21917
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, 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/interactTrack.c
  • lines changed 25, context: html, text, full: html, text
    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
  • lines changed 77, context: html, text, full: html, text
    442fef159db4b61a41789813c9068776ef2f8cfb Mon Sep 17 19:39:24 2018 -0700
    Pack mode. refs #21917
  • lines changed 9, 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
  • 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
  • lines changed 69, 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
  • lines changed 13, 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
  • lines changed 4, 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
  • lines changed 155, context: html, text, full: html, text
    39e533cc9ffcb46d9c484dc09a387a031a739391 Mon Sep 24 16:35:53 2018 -0700
    Updating from master
  • lines changed 277, 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
  • lines changed 1, context: html, text, full: html, text
    0a037dc34719826e667970a3f7dc99140cc4eef6 Wed Sep 26 10:49:12 2018 -0700
    Fix pack mode on cross-chrom item. refs #21917
  • lines changed 9, context: html, text, full: html, text
    cde6d1587f5f3b2f56de5c45125f42c24cfde4a3 Wed Sep 26 15:48:58 2018 -0700
    Support interchromosomal items in merge mode. refs #21917
  • lines changed 1, 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
  • lines changed 13, context: html, text, full: html, text
    229b9f6993152bab7202c2a32f461ecaa478e140 Mon Oct 1 16:28:22 2018 -0700
    Rename merge mode to cluster mode. refs #21917
  • lines changed 22, 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/simpleTracks.c
  • lines changed 19, 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
  • 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/hgc/interactClick.c
  • lines changed 37, 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
  • lines changed 26, context: html, text, full: html, text
    1626a52b02dcd43ea663946afc3f296a8ce9257b Wed Sep 26 16:38:26 2018 -0700
    Add click support to merged interactionss. refs #21917
  • lines changed 17, context: html, text, full: html, text
    b87966ef79a5c54ed61f83bc59233f1628cd7ac7 Wed Sep 26 17:02:49 2018 -0700
    More click support for merged interactions. refs #21917
  • lines changed 14, context: html, text, full: html, text
    229b9f6993152bab7202c2a32f461ecaa478e140 Mon Oct 1 16:28:22 2018 -0700
    Rename merge mode to cluster mode. refs #21917
  • lines changed 5, context: html, text, full: html, text
    e8d73d075f5667438415ec1e549cd9df8efe499a Tue Oct 2 14:31:45 2018 -0700
    Fix details in cluster mode. refs #21917
  • lines changed 4, 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/inc/interact.h
  • lines changed 9, context: html, text, full: html, text
    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
  • lines changed 6, context: html, text, full: html, text
    442fef159db4b61a41789813c9068776ef2f8cfb Mon Sep 17 19:39:24 2018 -0700
    Pack mode. refs #21917
  • lines changed 3, 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
  • lines changed 17, context: html, text, full: html, text
    39e533cc9ffcb46d9c484dc09a387a031a739391 Mon Sep 24 16:35:53 2018 -0700
    Updating from master
• src/hg/inc/interactUi.h
  • lines changed 9, 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
  • lines changed 10, 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/lib/interact.c
  • lines changed 106, context: html, text, full: html, text
    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
  • lines changed 68, context: html, text, full: html, text
    442fef159db4b61a41789813c9068776ef2f8cfb Mon Sep 17 19:39:24 2018 -0700
    Pack mode. refs #21917
  • lines changed 56, 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
  • lines changed 2, 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
  • lines changed 193, context: html, text, full: html, text
    39e533cc9ffcb46d9c484dc09a387a031a739391 Mon Sep 24 16:35:53 2018 -0700
    Updating from master
  • lines changed 36, 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
  • lines changed 17, 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
  • lines changed 1, 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/lib/interactUi.c
  • lines changed 66, 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
  • lines changed 26, 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/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    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/makeDb/trackDb/human/geneHancer.html
  • lines changed 51, 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
  • lines changed 91, 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
  • lines changed 93, context: html, text, full: html, text
    ddaf683e4f99f8b8173d4d045db1ba9222e3447c Tue Oct 2 18:26:49 2018 -0700
    Reorg to follow section conventions. refs #21917
  • lines changed 25, 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/hg19/trackDb.geneHancer.ra
  • lines changed 1, context: html, text, full: html, text
    35460385dc428f5357f9232a0e83547e955f8285 Mon Sep 17 22:39:57 2018 -0700
    Fix error.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, 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/trackDb.geneHancer.ra
  • lines changed 29, 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
  • lines changed 12, context: html, text, full: html, text
    54e6ff68a081a4b6d7785d1329d48f67947e75bf Mon Oct 1 16:29:24 2018 -0700
    Rename merge mode to cluster mode. refs #21917
  • lines changed 4, context: html, text, full: html, text
    74f1973502355135843e87d38fec2019a0eaed73 Tue Oct 2 13:57:26 2018 -0700
    Fix defaults (set to DoubleElite subset). refs #22048
  • lines changed 2, context: html, text, full: html, text
    61981d22590032673103aa71408faa4842466dd8 Tue Oct 2 14:32:12 2018 -0700
    Add URL to cluster mode. refs #21917
  • lines changed 1, 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