All File Changes

v362_preview to v362_preview2 (2018-02-19 to 2018-02-26) v362

• confs/hgwdev.hg.conf
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    301febfc75880b9e69e71373f411cb110db4038d Sun Feb 25 01:11:48 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 5, context: html, text, full: html, text
    fe0f5e6f44da6757e1a12312a875c98af7396278 Wed Feb 21 12:51:23 2018 -0800
    GBIB: Fixing typo in R install and fixing genome-euro redirect after more feedback from Gokhul
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 2, context: html, text, full: html, text
    20dcd5da48502709c544cc78a8264e8964d1449e Thu Feb 22 11:32:28 2018 -0800
    CIRM: making error message better, for Matt's QA scripts.
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 3, context: html, text, full: html, text
    8d94c34dea78b09a156f07331df43aa0114b9420 Mon Feb 26 07:53:20 2018 -0800
    Updating picture for Ecker. Correcting name spelling, no redmine
• src/hg/cirm/gateway/htdocs/images/piPortraits/JoeEcker_CIRM.jpg
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    f547d72f99e1d41e26d477ac6ebbc9687faf3b55 Fri Feb 23 14:42:19 2018 -0800
    Adding requested image of Joe Ecker, no redmine
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 1, context: html, text, full: html, text
    9f18fac08569e0380493fd9305fcc51db3d24b6d Mon Feb 26 08:11:44 2018 -0800
    Minor correction to div tag at top of footer. Added styles to makefile. Minor changes to cirmStyle.css to make title bars have rounded edges. no redmine
• src/hg/cirm/gateway/htdocs/makefile
  • lines changed 3, context: html, text, full: html, text
    9f18fac08569e0380493fd9305fcc51db3d24b6d Mon Feb 26 08:11:44 2018 -0800
    Minor correction to div tag at top of footer. Added styles to makefile. Minor changes to cirmStyle.css to make title bars have rounded edges. no redmine
• src/hg/cirm/gateway/htdocs/style/cirmStyle.css
  • lines changed 2, context: html, text, full: html, text
    9f18fac08569e0380493fd9305fcc51db3d24b6d Mon Feb 26 08:11:44 2018 -0800
    Minor correction to div tag at top of footer. Added styles to makefile. Minor changes to cirmStyle.css to make title bars have rounded edges. no redmine
• src/hg/hgCollection/hgCollection.c
  • lines changed 13, context: html, text, full: html, text
    6c0552193a83587fccb506d9d687e57b754d44b2 Wed Feb 21 13:20:40 2018 -0800
    be more exact about what tracks are in the visible tracks folder.
  • lines changed 165, context: html, text, full: html, text
    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 5, context: html, text, full: html, text
    4c4bf5f31b6f0aa1549778dc06caad4d84ed4966 Tue Feb 20 18:02:40 2018 -0800
    hgHubConnect now assembles search results a bit faster (turns out there can be enough hits per hub that head vs tail insertion makes a difference). refs #18865
• src/hg/hgPcr/hgPcr.c
  • lines changed 4, context: html, text, full: html, text
    411f45b8bd4a6cde404a78b81e4a41ea0aede025 Mon Feb 26 07:51:10 2018 -0800
    Adding link to YouTube video about using hgPcr, refs #20952
• src/hg/hgTables/custom.c
  • lines changed 6, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTables/joining.c
  • lines changed 1, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTables/schema.c
  • lines changed 7, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTracks/bedTrack.c
  • lines changed 3, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTracks/hgTracks.c
  • lines changed 14, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
  • lines changed 2, context: html, text, full: html, text
    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 3, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgTracks/interactTrack.c
  • lines changed 316, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 24, context: html, text, full: html, text
    b1ae6aafe2f0997af978f7984c270fbe3c1edb4a Wed Jan 17 17:40:46 2018 -0800
    Add feature to draw dotted lines for reverse direction interactions. refs #17512
  • lines changed 10, context: html, text, full: html, text
    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
  • lines changed 9, context: html, text, full: html, text
    dc12783aae8e908620e0c768f7c9d03e5142858c Sun Jan 28 19:58:53 2018 -0800
    More fixes to other chrom labels. refs #17512
  • lines changed 3, context: html, text, full: html, text
    112e6092522e4eed411c8b64c225e792bbb640a0 Mon Jan 29 09:08:28 2018 -0800
    Tweak height of curves to maintain shape while remaining comparability to off-screen endpoint lines. refs #117512
  • lines changed 89, context: html, text, full: html, text
    34c07fa95c834c1377e4e185b1a9e19499a0d536 Tue Jan 30 15:48:56 2018 -0800
    Update schema, based on input from Braney. Improve map boxes. refs #17512
  • lines changed 8, context: html, text, full: html, text
    3032095fbd5dafc5cc96d4ba375e215c9a7bd745 Tue Jan 30 16:27:15 2018 -0800
    Change dotted lines to dashed for better visibility. Suggestion by JK. refs #17512
  • lines changed 12, context: html, text, full: html, text
    fa8c6c2c8140538f014381e43421163cc6c7eb98 Wed Jan 31 15:22:00 2018 -0800
    Flesh out details page for interact track. refs #17512
  • lines changed 29, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
  • lines changed 2, context: html, text, full: html, text
    f073f78c136793c533aa903387ca622b4f2203c6 Fri Feb 23 10:18:29 2018 -0800
    Fixing compiler -O warning about uninitialized variables.
• src/hg/hgTracks/longRangeTrack.c
  • lines changed 29, context: html, text, full: html, text
    e3ab5bcc4bf9024a1c21c8ad5f7ef21ffc9a67cc Wed Jan 3 15:21:09 2018 -0800
    Add curve drawing (ellipse and bezier). Code by Zingl Alois, 2016, posted to github and http://members.chello.at/~easyfilter/bresenham.html. refs #17512
  • lines changed 53, context: html, text, full: html, text
    cae6dcfc9c025d79e0ab8062232f1c3b9592d2da Thu Jan 4 16:54:32 2018 -0800
    Add cart var to switch interaction drawing style. interaction=line|curve|ellipse. Useful during dev, maybe promote to feature. Code cleanup. refs #17512
  • lines changed 2, context: html, text, full: html, text
    3bae4c349bcfe87d5d8c8937b59fc8d00f585bf0 Mon Jan 8 16:00:19 2018 -0800
    Use anti-aliasing code for bezier curve. For shared dev w/ Braney. refs #17512
  • lines changed 2, context: html, text, full: html, text
    93fe466f71fc1e40c33e27f311f846d26028cb26 Thu Jan 11 18:18:16 2018 -0800
    Abandon unaliased bezier curve after Braney fixed aliased version. Checked timing on aliased and it was speedy, so ono reason to keep ugly drawer. refs #17512
  • lines changed 1, context: html, text, full: html, text
    d47135580518b138a64b785eddbc65891e48be21 Fri Jan 12 10:13:52 2018 -0800
    Integrate antialiased ellipse code. Awaits antialiasing fix from Braney. refs #17512
  • lines changed 3, context: html, text, full: html, text
    b1ae6aafe2f0997af978f7984c270fbe3c1edb4a Wed Jan 17 17:40:46 2018 -0800
    Add feature to draw dotted lines for reverse direction interactions. refs #17512
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 5, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    fac6f1db370338b0f775b60037e66fc2aac3cfdd Tue Jan 30 16:54:25 2018 -0800
    Beginnings of details page for interact track. refs #17512
  • lines changed 97, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    fac6f1db370338b0f775b60037e66fc2aac3cfdd Tue Jan 30 16:54:25 2018 -0800
    Beginnings of details page for interact track. refs #17512
• src/hg/hgc/interactClick.c
  • lines changed 155, context: html, text, full: html, text
    fac6f1db370338b0f775b60037e66fc2aac3cfdd Tue Jan 30 16:54:25 2018 -0800
    Beginnings of details page for interact track. refs #17512
  • lines changed 111, context: html, text, full: html, text
    fa8c6c2c8140538f014381e43421163cc6c7eb98 Wed Jan 31 15:22:00 2018 -0800
    Flesh out details page for interact track. refs #17512
  • lines changed 64, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    fac6f1db370338b0f775b60037e66fc2aac3cfdd Tue Jan 30 16:54:25 2018 -0800
    Beginnings of details page for interact track. refs #17512
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 1, context: html, text, full: html, text
    4c93f04ee11008a59d3e3022bcadef009c952d5b Fri Feb 16 13:52:57 2018 -0800
    adding link to dockerfile from mirror docs, after suggestion from zlab, refs #15174
• src/hg/htdocs/images/hgCollectionMouseOver.jpg
  • lines changed 0, context: html, text, full: html, text
    b4701e3fdcea71208a9d21034faa540ae5597b18 Fri Feb 23 16:38:33 2018 -0800
    More edits to hgCollect help. Will be adding a few more changes and additional pics. refs #11630
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 5, context: html, text, full: html, text
    b4701e3fdcea71208a9d21034faa540ae5597b18 Fri Feb 23 16:38:33 2018 -0800
    More edits to hgCollect help. Will be adding a few more changes and additional pics. refs #11630
  • lines changed 5, context: html, text, full: html, text
    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 89, context: html, text, full: html, text
    b4701e3fdcea71208a9d21034faa540ae5597b18 Fri Feb 23 16:38:33 2018 -0800
    More edits to hgCollect help. Will be adding a few more changes and additional pics. refs #11630
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    0b6ca6827857d15705fb41028e8938c82aae9d3e Mon Jan 8 16:01:06 2018 -0800
    Add standard box config. refs #17512
• src/hg/inc/hvGfx.h
  • lines changed 34, context: html, text, full: html, text
    e3ab5bcc4bf9024a1c21c8ad5f7ef21ffc9a67cc Wed Jan 3 15:21:09 2018 -0800
    Add curve drawing (ellipse and bezier). Code by Zingl Alois, 2016, posted to github and http://members.chello.at/~easyfilter/bresenham.html. refs #17512
  • lines changed 7, context: html, text, full: html, text
    93fe466f71fc1e40c33e27f311f846d26028cb26 Thu Jan 11 18:18:16 2018 -0800
    Abandon unaliased bezier curve after Braney fixed aliased version. Checked timing on aliased and it was speedy, so ono reason to keep ugly drawer. refs #17512
  • lines changed 2, context: html, text, full: html, text
    d47135580518b138a64b785eddbc65891e48be21 Fri Jan 12 10:13:52 2018 -0800
    Integrate antialiased ellipse code. Awaits antialiasing fix from Braney. refs #17512
  • lines changed 19, context: html, text, full: html, text
    b1ae6aafe2f0997af978f7984c270fbe3c1edb4a Wed Jan 17 17:40:46 2018 -0800
    Add feature to draw dotted lines for reverse direction interactions. refs #17512
  • lines changed 2, context: html, text, full: html, text
    3032095fbd5dafc5cc96d4ba375e215c9a7bd745 Tue Jan 30 16:27:15 2018 -0800
    Change dotted lines to dashed for better visibility. Suggestion by JK. refs #17512
• src/hg/inc/interact.h
  • lines changed 91, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 14, context: html, text, full: html, text
    34c07fa95c834c1377e4e185b1a9e19499a0d536 Tue Jan 30 15:48:56 2018 -0800
    Update schema, based on input from Braney. Improve map boxes. refs #17512
  • lines changed 3, context: html, text, full: html, text
    fa8c6c2c8140538f014381e43421163cc6c7eb98 Wed Jan 31 15:22:00 2018 -0800
    Flesh out details page for interact track. refs #17512
  • lines changed 3, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/inc/interactUi.h
  • lines changed 16, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 10, context: html, text, full: html, text
    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
  • lines changed 2, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    31822fe501d11cd0e9409d31d322c37aa63d6341 Fri Feb 23 14:44:57 2018 -0800
    changes in response to code review #20986
• src/hg/js/hgCollection.js
  • lines changed 4, context: html, text, full: html, text
    5df85e75e5ad83445d5fd90b5bd698f4bd4f315b Tue Feb 20 14:29:21 2018 -0800
    warn the user if there are no collections and they try to add to one with the "add" menu
  • lines changed 22, context: html, text, full: html, text
    df5f3339825d35ba2290bece7195045352ca9471 Wed Feb 21 10:09:17 2018 -0800
    fix problems when moving nodes causes a collection to be empty, or no longer empty
  • lines changed 4, context: html, text, full: html, text
    c5759cbf3e763c7248d0630001a7eebda9ed78d5 Wed Feb 21 10:34:31 2018 -0800
    don't let user's move the "empty collection" stub around
  • lines changed 67, context: html, text, full: html, text
    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    31822fe501d11cd0e9409d31d322c37aa63d6341 Fri Feb 23 14:44:57 2018 -0800
    changes in response to code review #20986
• src/hg/lib/customFactory.c
  • lines changed 215, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
  • lines changed 9, context: html, text, full: html, text
    c845037771404a9b1e7abd6e1368a02a2af47002 Tue Feb 20 08:10:00 2018 -0800
    fix recognition of doWiggle, and don't output some limits for custom composites because we don't have them.
  • lines changed 2, context: html, text, full: html, text
    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
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    5bb4dbb87b67606711b462855f64f31841b21a52 Thu Feb 22 09:03:00 2018 -0800
    Merge branch 'lr-arc-schema'
• src/hg/lib/hvGfx.c
  • lines changed 288, context: html, text, full: html, text
    f16d7206f27f0ed5965f791cf4e85dbc846ae31f Wed Jan 3 15:28:13 2018 -0800
    Preliminary (rough) support for curve drawing -- ellipse and bezier. Code by Zingl Alois, 2016, posted to github and http://members.chello.at/~easyfilter/bresenham.html. refs #17512
  • lines changed 3, context: html, text, full: html, text
    220096c307e85318afc75fd4c6c89b8259bbabfe Wed Jan 10 07:47:21 2018 -0800
    call mixDot correctly when drawing anti-aliased curves
  • lines changed 41, context: html, text, full: html, text
    93fe466f71fc1e40c33e27f311f846d26028cb26 Thu Jan 11 18:18:16 2018 -0800
    Abandon unaliased bezier curve after Braney fixed aliased version. Checked timing on aliased and it was speedy, so ono reason to keep ugly drawer. refs #17512
  • lines changed 78, context: html, text, full: html, text
    d47135580518b138a64b785eddbc65891e48be21 Fri Jan 12 10:13:52 2018 -0800
    Integrate antialiased ellipse code. Awaits antialiasing fix from Braney. refs #17512
  • lines changed 85, context: html, text, full: html, text
    c22e9170ef4e25c0eb5cd75c8988537d1a27aabe Wed Jan 17 16:22:42 2018 -0800
    Removing antialiased ellipse code -- too buggy. refs #17512
  • lines changed 108, context: html, text, full: html, text
    b1ae6aafe2f0997af978f7984c270fbe3c1edb4a Wed Jan 17 17:40:46 2018 -0800
    Add feature to draw dotted lines for reverse direction interactions. refs #17512
  • lines changed 41, context: html, text, full: html, text
    3032095fbd5dafc5cc96d4ba375e215c9a7bd745 Tue Jan 30 16:27:15 2018 -0800
    Change dotted lines to dashed for better visibility. Suggestion by JK. refs #17512
• src/hg/lib/interact.as
  • lines changed 21, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 15, context: html, text, full: html, text
    34c07fa95c834c1377e4e185b1a9e19499a0d536 Tue Jan 30 15:48:56 2018 -0800
    Update schema, based on input from Braney. Improve map boxes. refs #17512
• src/hg/lib/interact.c
  • lines changed 240, context: html, text, full: html, text
    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
  • lines changed 54, context: html, text, full: html, text
    34c07fa95c834c1377e4e185b1a9e19499a0d536 Tue Jan 30 15:48:56 2018 -0800
    Update schema, based on input from Braney. Improve map boxes. refs #17512
  • lines changed 9, context: html, text, full: html, text
    fa8c6c2c8140538f014381e43421163cc6c7eb98 Wed Jan 31 15:22:00 2018 -0800
    Flesh out details page for interact track. refs #17512
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/lib/interact.sql
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    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
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    34c07fa95c834c1377e4e185b1a9e19499a0d536 Tue Jan 30 15:48:56 2018 -0800
    Update schema, based on input from Braney. Improve map boxes. refs #17512
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/lib/interactUi.c
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    62e7108fa6040d801ee42c10ef0b1381b0401d5a Sun Jan 28 19:32:46 2018 -0800
    Add track height control. refs #17512
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    95f186679b2dad838b39836189cbf4eb2a054309 Tue Jan 30 16:28:22 2018 -0800
    Change UI wording (line->rectangle), as per AnnZ suggestion. refs #17512
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/lib/longRange.c
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    0b6ca6827857d15705fb41028e8938c82aae9d3e Mon Jan 8 16:01:06 2018 -0800
    Add standard box config. refs #17512
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    6498200fbad339b838d39598627392cb254ad476 Mon Jan 8 17:04:12 2018 -0800
    Fix setting view height. refs #17512
• src/hg/lib/makefile
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    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
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    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
• src/hg/lib/trackDbCustom.c
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    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
• src/hg/lib/trackHub.c
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
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    31822fe501d11cd0e9409d31d322c37aa63d6341 Fri Feb 23 14:44:57 2018 -0800
    changes in response to code review #20986
• src/hg/lib/variantProjector.c
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    f9e9dc9fe43953f72b43314aba821045a601ee3c Tue Feb 20 14:16:59 2018 -0800
    Add support for PSL with double-sided gaps to pslIntronTooShort and pslNmdTarget. refs #20948
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    95be7a6a29674ae32b5f1d8eddb079160054bc86 Thu Feb 22 09:55:32 2018 -0800
    genomeTxMismatch was supposed to ignore indels and just find base mismatches, but it wasn't ignoring genomic deletions, so sometimes indel-shifting wasn't performed as expected. This has the effect of reducing the range of no-change in PTV035. refs #20948
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    11e141539ac33a2571e5422a3723046d49a60644 Fri Feb 23 09:53:40 2018 -0800
    Oops, compare shiftR to the block size to the right not left. refs #20948
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    b280a09989c0816d3c81c13e284c298b420edc1f Fri Feb 23 15:09:46 2018 -0800
    Thanks Jonathan for pointing out that I should update the errAbort message. refs #20988
• src/hg/makeDb/hgLoadBed/makefile
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/makeDb/schema/all.joiner
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    9464ea323c5773003cff696c3470f72a5c5b4e60 Tue Feb 20 09:19:03 2018 -0800
    Commenting out database specifier for ncbiRefSeq after discussion with Angie
• src/hg/makeDb/trackDb/acembly.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/affyAllExonProbes.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/blastDm1FB.html
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    8bb61e0c3c82e8818df35001bba7bed3fa4a337f Tue Feb 20 10:07:11 2018 -0800
    Fixing broken links for dp2, no Redmine.
• src/hg/makeDb/trackDb/blastDm2FB.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/blastHg18KG.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/ccdsGene.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/chainDm3.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/chainNet.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
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    5cfa976169ba01f1f9e568ab9fbb17002b3e756b Thu Feb 22 09:24:41 2018 -0800
    Fixing broken links for panTro3, no Redmine.
• src/hg/makeDb/trackDb/chimp/panTro3/gold.html
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    5cfa976169ba01f1f9e568ab9fbb17002b3e756b Thu Feb 22 09:24:41 2018 -0800
    Fixing broken links for panTro3, no Redmine.
• src/hg/makeDb/trackDb/drosophila/chainDm1.html
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    8bb61e0c3c82e8818df35001bba7bed3fa4a337f Tue Feb 20 10:07:11 2018 -0800
    Fixing broken links for dp2, no Redmine.
• src/hg/makeDb/trackDb/drosophila/droEre1/gap.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/drosophila/xenoMrna.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/drosophila/xenoRefGene.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/est.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
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    a80a8de2fc8f3573cd184b2a4032afff1f959e16 Wed Jan 17 16:19:15 2018 -0800
    First cut of interact track type. Same display as longTabix, but with new schema to support phase 2 features. refs #17512
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    e5a2eedb0c397971feac1ab56c8cbefe496ff309 Sun Jan 28 19:20:16 2018 -0800
    Add track UI to change drawing mode (line, ellipse, curve). Fix to other chromosome labeling (still some probs left). refs #17512
• src/hg/makeDb/trackDb/intronEst.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/affyGnf1m.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/bacEndPairs.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/genotypeArrays.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/stsMapMouseNew.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mouse/xenoRefGene.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/mrna.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/netDm1.html
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    8bb61e0c3c82e8818df35001bba7bed3fa4a337f Tue Feb 20 10:07:11 2018 -0800
    Fixing broken links for dp2, no Redmine.
• src/hg/makeDb/trackDb/netDm3.html
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    f27cc150b619c51277ea5b4efd5e6834e03271a6 Fri Feb 23 13:07:34 2018 -0800
    Fixing broken links for droEre1, no Redmine.
• src/hg/makeDb/trackDb/nscanGene.html
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    5cfa976169ba01f1f9e568ab9fbb17002b3e756b Thu Feb 22 09:24:41 2018 -0800
    Fixing broken links for panTro3, no Redmine.
• src/hg/makeDb/trackDb/pubs.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/refGene.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/snp128.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/trackDb.ra
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    3e135cebc8f3de90c20312e9427e963c14feaee8 Fri Feb 23 16:54:25 2018 -0800
    changing crispr track from superTrack to a composite, after comment from Bob based on workshop, no redmine
• src/hg/makeDb/trackDb/transMapAlnMRna.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/transMapAlnRefSeq.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
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    efc73f932c7e0432ec4cd4eaf3c16d816b618607 Wed Feb 21 10:06:55 2018 -0800
    Fixing broken links for mm9, no Redmine.
• src/hg/makeDb/trackDb/xenoMrna.html
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    5cfa976169ba01f1f9e568ab9fbb17002b3e756b Thu Feb 22 09:24:41 2018 -0800
    Fixing broken links for panTro3, no Redmine.
• src/hg/makeDb/trackDb/xenoRefGene.html
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    5cfa976169ba01f1f9e568ab9fbb17002b3e756b Thu Feb 22 09:24:41 2018 -0800
    Fixing broken links for panTro3, no Redmine.
• src/hg/utils/hubCheck/hubCheck.c
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    6f726d2bcdb4fca993c06cf2181dce97b061702d Thu Feb 22 08:59:49 2018 -0800
    Add support for custom tracks and hub tracks. refs #17512
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
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    95be7a6a29674ae32b5f1d8eddb079160054bc86 Thu Feb 22 09:55:32 2018 -0800
    genomeTxMismatch was supposed to ignore indels and just find base mismatches, but it wasn't ignoring genomic deletions, so sometimes indel-shifting wasn't performed as expected. This has the effect of reducing the range of no-change in PTV035. refs #20948
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf
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    95be7a6a29674ae32b5f1d8eddb079160054bc86 Thu Feb 22 09:55:32 2018 -0800
    genomeTxMismatch was supposed to ignore indels and just find base mismatches, but it wasn't ignoring genomic deletions, so sometimes indel-shifting wasn't performed as expected. This has the effect of reducing the range of no-change in PTV035. refs #20948
• src/lib/annoStreamVcf.c
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    3cdb290e612b39be6cc8073bb17112c6c1385a13 Wed Feb 21 11:28:22 2018 -0800
    Yikes, forgetting to update a loop variable caused subsequent chroms' records to be overlooked when restricting to a region. Big VCFs are usually single-chrom, I guess that's why the bug has been under the radar until now.
• src/lib/htmshell.c
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    9a24eab7aa53e82ca200d92f532411f37d8487f3 Sat Feb 24 18:09:09 2018 -0800
    add lazy loading to hgCollection, modify CSP policy to allow blob:
• src/utils/qa/weeklybld/buildEnv.csh
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    13b84083ef2ab5745c44cb3fc2e00a7da73fb572 Mon Feb 26 10:01:40 2018 -0800
    v362 preview2 refs #20999

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