All File Changes

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

• confs/hgwbeta.hg.conf
  • lines changed 28, context: html, text, full: html, text
    25ae1d9144c6f8da78beaf03aac3efbf8ac946b6 Sun Oct 7 01:11:38 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 24, context: html, text, full: html, text
    25ae1d9144c6f8da78beaf03aac3efbf8ac946b6 Sun Oct 7 01:11:38 2018 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 11, context: html, text, full: html, text
    25ae1d9144c6f8da78beaf03aac3efbf8ac946b6 Sun Oct 7 01:11:38 2018 -0700
    Installing updated hg.conf files from UCSC servers
• java/build.xml
  • lines changed 2, context: html, text, full: html, text
    45bf45d5deac830c90a6c382ed3a2f53fff251b6 Mon Oct 1 14:25:16 2018 -0700
    stop special casing jtidy (fixes TrackCheck problem )
• src/hg/cirm/gateway/htdocs/bestPractices.html
  • lines changed 54, context: html, text, full: html, text
    efe31a5b022d2db997406571f7a9576ab48bc87f Mon Oct 1 15:49:02 2018 -0700
    First pass as a CIRM best practices page, refs #21020
  • lines changed 3, context: html, text, full: html, text
    c4bc84c4af12e33d6876d55a624e020d060a68cf Tue Oct 2 09:15:49 2018 -0700
    Adding Best Practices page to header, changing tool tips for a few assays, fixing best practices page header, refs #21020 #22154
• src/hg/cirm/gateway/htdocs/images/assay.png
  • lines changed 0, context: html, text, full: html, text
    7d354381c210077e36817d34eeb0eb406e9f2354 Mon Oct 1 15:37:48 2018 -0700
    Adding best practices images, refs #21020
• src/hg/cirm/gateway/htdocs/images/bestPracticesPt1.png
  • lines changed 0, context: html, text, full: html, text
    1ac00f0b537928ff3043aa9114b1461e35b49f20 Wed Oct 3 15:50:50 2018 -0700
    Adding new images for best practices page, refs #21020
• src/hg/cirm/gateway/htdocs/images/bestPracticesPt2.png
  • lines changed 0, context: html, text, full: html, text
    1ac00f0b537928ff3043aa9114b1461e35b49f20 Wed Oct 3 15:50:50 2018 -0700
    Adding new images for best practices page, refs #21020
• src/hg/cirm/gateway/htdocs/images/lifeStage.png
  • lines changed 0, context: html, text, full: html, text
    7d354381c210077e36817d34eeb0eb406e9f2354 Mon Oct 1 15:37:48 2018 -0700
    Adding best practices images, refs #21020
• src/hg/cirm/gateway/htdocs/images/reprogrammingAndDiff.png
  • lines changed 0, context: html, text, full: html, text
    7d354381c210077e36817d34eeb0eb406e9f2354 Mon Oct 1 15:37:48 2018 -0700
    Adding best practices images, refs #21020
• src/hg/cirm/gateway/htdocs/images/workflow.png
  • lines changed 0, context: html, text, full: html, text
    7d354381c210077e36817d34eeb0eb406e9f2354 Mon Oct 1 15:37:48 2018 -0700
    Adding best practices images, refs #21020
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 2, context: html, text, full: html, text
    c4bc84c4af12e33d6876d55a624e020d060a68cf Tue Oct 2 09:15:49 2018 -0700
    Adding Best Practices page to header, changing tool tips for a few assays, fixing best practices page header, refs #21020 #22154
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 10, context: html, text, full: html, text
    c4bc84c4af12e33d6876d55a624e020d060a68cf Tue Oct 2 09:15:49 2018 -0700
    Adding Best Practices page to header, changing tool tips for a few assays, fixing best practices page header, refs #21020 #22154
• 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/config.c
  • lines changed 5, context: html, text, full: html, text
    07d9e9ec22f32d628d1298245cf7852b2015a5e6 Tue Oct 2 11:42:23 2018 -0700
    Multi-region config also needs to watch out for :start-end suffixes in {alt,fix}Locations.name. refs #22144
• 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/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    6bd8612735d974a18ca31e5ae71a7c7828c7fb88 Fri Oct 5 10:31:58 2018 -0700
    Editing FAQreleases.html;adding thaSir1, ref#16028
  • lines changed 2, context: html, text, full: html, text
    d053e14f659e53dcdb614380cf24ef75df46c3da Fri Oct 5 10:47:40 2018 -0700
    OviAri4 added to FAQreleases
  • lines changed 2, context: html, text, full: html, text
    a7b0fa98e5a458ddfea4cf35ee6e18671d1aeb3e Fri Oct 5 11:03:22 2018 -0700
    Adding anoGam3 to the FAQreleases.html page ref#20743
  • lines changed 2, context: html, text, full: html, text
    8206dcac7d374cff1fc611413d92340b348b69c6 Fri Oct 5 14:29:20 2018 -0700
    Adding panTro6 to the FAQreleases, refs #20979
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    fdd902e91bc4ca222a4a056e91da55e46cd91bbd Fri Oct 5 10:41:02 2018 -0700
    Adding oviAri4 to the credits list
  • lines changed 1, context: html, text, full: html, text
    a151c4a84ba3edfaeedf3bb0cba36fb467fd75f9 Fri Oct 5 10:46:33 2018 -0700
    Adding anoGam3 assembly to the credits page Ref#20743
  • lines changed 1, context: html, text, full: html, text
    543beef964c4ebba03246cec15887d49ee463c20 Fri Oct 5 10:53:35 2018 -0700
    Fixing the bullet points on anoGam3 ref#20743
  • lines changed 36, context: html, text, full: html, text
    1fc32feb290056fdf7c95e040cace555f0e19ae7 Fri Oct 5 11:09:09 2018 -0700
    adding thaSir1 to credits.html, refs#16028
  • lines changed 30, context: html, text, full: html, text
    3e1d699eb8c716b9921b41ab6985d427ebb51ce6 Fri Oct 5 16:26:28 2018 -0700
    Adding panTro6 credits to credits.html, refs #20979
• src/hg/htdocs/license/index.html
  • lines changed 4, context: html, text, full: html, text
    f2119ace0903af993bbc94f23415e213e2d9c824 Thu Oct 4 14:48:45 2018 -0700
    IP changed their preferred email address, refs #13978
• 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/doc/hg19.txt
  • lines changed 54, context: html, text, full: html, text
    4ab525cb676f72b212e3636bfd60b375f9ef1090 Tue Oct 2 13:28:56 2018 -0700
    First version of pLI and missense score track for hg19, more changes likely to come, refs #20394
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    3d0d0436effd29bb397bbb7fe7e1a1997dd1cdad Tue Oct 2 16:02:46 2018 -0700
    Turning on Genbank updates for hgwbeta, refs #20979
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    12c6529293d340d297c2e89f32e713e508195073 Fri Oct 5 16:07:18 2018 -0700
    more stuff to ignore
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    6d23f64f431b0164c61f26439d25d740cf3d0cbd Wed Oct 3 14:29:29 2018 -0700
    Added oviAri4 to rr.dbs
  • lines changed 2, context: html, text, full: html, text
    e5e4647ea62163a2e81bd8fa528eb3d7c420ca2f Thu Oct 4 14:59:36 2018 -0700
    Turning on Genbank updates for panTro6 on the RR, refs#20979
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 1, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/chainSelf.html
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    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/cytoBand.html
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    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• 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.gnomad.ra
  • lines changed 23, context: html, text, full: html, text
    4ab525cb676f72b212e3636bfd60b375f9ef1090 Tue Oct 2 13:28:56 2018 -0700
    First version of pLI and missense score track for hg19, more changes likely to come, refs #20394
• 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/hg38/centromeres.html
  • lines changed 1, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 5, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 5, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 5, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
  • lines changed 4, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 4, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/mappability.html
  • lines changed 3, context: html, text, full: html, text
    90aa59a99b7021c8600a1ec895c09e45cdcac9f8 Tue Oct 2 08:57:37 2018 -0700
    Updating redirected links, http to https, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.html
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    46734f435d23f6919a08661b386c5a70a01a51cc Tue Sep 25 12:00:32 2018 -0700
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