All File Changes

v380_preview2 to v380_base (2019-04-01 to 2019-04-08) v380

• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 15, context: html, text, full: html, text
    8aaedd5ea97c078e37e7634eea3dc996ff8528d9 Fri Apr 5 23:13:26 2019 -0700
    allowing exception for meta.txt, which is usually only directly used with maniSummary.txt, so that it will not try to remove an old symlink and create a new one when meta.txt will have NO symlinks.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    52052c9f3776cce6249a0cf819791a3ed49a9d87 Mon Apr 1 14:02:26 2019 -0700
    removing unused cirm-motd.html. Its functionality has migrated to the gateway.
• src/hg/cirm/cdw/cdwWebBrowse/cirm-motd.html
  • lines changed 5, context: html, text, full: html, text
    52052c9f3776cce6249a0cf819791a3ed49a9d87 Mon Apr 1 14:02:26 2019 -0700
    removing unused cirm-motd.html. Its functionality has migrated to the gateway.
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 19, context: html, text, full: html, text
    52052c9f3776cce6249a0cf819791a3ed49a9d87 Mon Apr 1 14:02:26 2019 -0700
    removing unused cirm-motd.html. Its functionality has migrated to the gateway.
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    410efbd4626c73d3e563ce3ddd86c3e867bc4216 Fri Apr 5 19:42:15 2019 -0700
    adding needed utility cdwChangeAccess to the makefile utils list
• src/hg/cirm/gateway/htdocs/cescg/cescgOrg.html
  • lines changed 8, context: html, text, full: html, text
    b58ec862d7bfa9371f05c460e54162e6c3c8dc40 Wed Apr 3 15:17:18 2019 -0700
    Adding anchor links for CESCG pages, refs #23013
  • lines changed 3, context: html, text, full: html, text
    1754e19178988cee425c7b344e82dff116127487 Thu Apr 4 11:25:54 2019 -0700
    Changing link style. Changing apostrophe character. refs #23172
• src/hg/cirm/gateway/htdocs/cescg/cescgPeople.html
  • lines changed 4, context: html, text, full: html, text
    b58ec862d7bfa9371f05c460e54162e6c3c8dc40 Wed Apr 3 15:17:18 2019 -0700
    Adding anchor links for CESCG pages, refs #23013
• src/hg/cirm/gateway/htdocs/cescg/cescgPubs.html
  • lines changed 6, context: html, text, full: html, text
    b58ec862d7bfa9371f05c460e54162e6c3c8dc40 Wed Apr 3 15:17:18 2019 -0700
    Adding anchor links for CESCG pages, refs #23013
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 5, context: html, text, full: html, text
    b220f64e24a111896b20a91bd7b509acbbce714e Wed Apr 3 14:27:10 2019 -0700
    Fixing some links, refs #23172
• src/hg/cirm/gateway/htdocs/js/cirmStuff.js
  • lines changed 2, context: html, text, full: html, text
    6ac2a1bd474342a25b2598f9843a8f6ec137b2d2 Thu Apr 4 17:50:45 2019 -0700
    Make sure the login menu shows up on hgwdev and its virtual hosts too.
  • lines changed 100, context: html, text, full: html, text
    9bdac22e315eb893cbc16ea6ad207e865e128382 Fri Apr 5 23:50:31 2019 -0700
    fixing cirm gateway makefiles. adding proper targets for user and alpha, moving js dir to be at same level as htdocs which is how genome browser does it. TODO versioned symlinks.
• src/hg/cirm/gateway/htdocs/makefile
  • lines changed 25, context: html, text, full: html, text
    9bdac22e315eb893cbc16ea6ad207e865e128382 Fri Apr 5 23:50:31 2019 -0700
    fixing cirm gateway makefiles. adding proper targets for user and alpha, moving js dir to be at same level as htdocs which is how genome browser does it. TODO versioned symlinks.
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 26, context: html, text, full: html, text
    2da177033ff3eb8e5c359fc3254c3be92d447c59 Tue Apr 2 11:18:49 2019 -0700
    Adding paper and database links for two kriegstein datasets. refs #23155
  • lines changed 37, context: html, text, full: html, text
    36df922e980c425f723818544ddd210d59cd0cd4 Wed Apr 3 10:37:22 2019 -0700
    added link for kriegstienBrainOrganoids2. refs #23242
  • lines changed 46, context: html, text, full: html, text
    ede58f65bb4b32788dcfabafbcb04f1dfab4fe66 Wed Apr 3 13:13:07 2019 -0700
    Adding links for assay info icons in table header.
  • lines changed 59, context: html, text, full: html, text
    63a95bfe1026e5097a22bf8d334c4de4380cb9a5 Wed Apr 3 14:03:49 2019 -0700
    Adding links to download files for a dataset to projects page. refs #23124
• src/hg/cirm/gateway/htdocs/style/makefile
  • lines changed 26, context: html, text, full: html, text
    9bdac22e315eb893cbc16ea6ad207e865e128382 Fri Apr 5 23:50:31 2019 -0700
    fixing cirm gateway makefiles. adding proper targets for user and alpha, moving js dir to be at same level as htdocs which is how genome browser does it. TODO versioned symlinks.
• src/hg/cirm/gateway/js/cirmStuff.js
  • lines changed 100, context: html, text, full: html, text
    9bdac22e315eb893cbc16ea6ad207e865e128382 Fri Apr 5 23:50:31 2019 -0700
    fixing cirm gateway makefiles. adding proper targets for user and alpha, moving js dir to be at same level as htdocs which is how genome browser does it. TODO versioned symlinks.
• src/hg/cirm/gateway/js/makefile
  • lines changed 32, context: html, text, full: html, text
    9bdac22e315eb893cbc16ea6ad207e865e128382 Fri Apr 5 23:50:31 2019 -0700
    fixing cirm gateway makefiles. adding proper targets for user and alpha, moving js dir to be at same level as htdocs which is how genome browser does it. TODO versioned symlinks.
• src/hg/hgTables/hgTables.c
  • lines changed 56, context: html, text, full: html, text
    7c459941c1e589297e0014bf7957599f70836096 Thu Apr 4 11:08:18 2019 -0700
    moving some SQL functions to jksql.c from hgTables refs #18869 #23233
• src/hg/hgTables/hgTables.h
  • lines changed 14, context: html, text, full: html, text
    7c459941c1e589297e0014bf7957599f70836096 Thu Apr 4 11:08:18 2019 -0700
    moving some SQL functions to jksql.c from hgTables refs #18869 #23233
• src/hg/hgTables/schema.c
  • lines changed 16, context: html, text, full: html, text
    7c459941c1e589297e0014bf7957599f70836096 Thu Apr 4 11:08:18 2019 -0700
    moving some SQL functions to jksql.c from hgTables refs #18869 #23233
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
• src/hg/hgTracks/lollipop.c
  • lines changed 160, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
• src/hg/hgTracks/lolly.c
  • lines changed 160, context: html, text, full: html, text
    ae8dc8ab5e2c121398f31531c701ea064fb19aeb Thu Apr 4 07:05:40 2019 -0700
    add the ability to search the MANE track
  • lines changed 84, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
  • lines changed 54, context: html, text, full: html, text
    a74afbfcfe01da0f925d8ff976cf5f2f13ce967d Sat Apr 6 16:23:21 2019 -0700
    more lolly work
  • lines changed 23, context: html, text, full: html, text
    d3875e2d3ebe45f89214d98a2c766a3771e7b057 Sun Apr 7 15:05:54 2019 -0700
    add manual view limits to lolly
  • lines changed 6, context: html, text, full: html, text
    b973bf71d1f2ed60125517f6fa69923a6faca7fa Sun Apr 7 15:55:16 2019 -0700
    add bigBed filtering to bigLolly
  • lines changed 2, context: html, text, full: html, text
    aa8e1b3f010a3baa78d4d2a8c331ebf4aaa2d3aa Sun Apr 7 16:53:25 2019 -0700
    make bigLolly filtering more efficient
• src/hg/hgTracks/lolly.h
  • lines changed 14, context: html, text, full: html, text
    ae8dc8ab5e2c121398f31531c701ea064fb19aeb Thu Apr 4 07:05:40 2019 -0700
    add the ability to search the MANE track
  • lines changed 4, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
  • lines changed 2, context: html, text, full: html, text
    d3875e2d3ebe45f89214d98a2c766a3771e7b057 Sun Apr 7 15:05:54 2019 -0700
    add manual view limits to lolly
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
  • lines changed 2, context: html, text, full: html, text
    a74afbfcfe01da0f925d8ff976cf5f2f13ce967d Sat Apr 6 16:23:21 2019 -0700
    more lolly work
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    a74afbfcfe01da0f925d8ff976cf5f2f13ce967d Sat Apr 6 16:23:21 2019 -0700
    more lolly work
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 4, context: html, text, full: html, text
    36539fdc6ab8ccb4b4beb69464ffcffabffcaf85 Thu Apr 4 15:03:14 2019 -0700
    Adding an extra definition to GENCODE basic no RM
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 10, context: html, text, full: html, text
    d7b4748a91dc6442607af5c9a3c0c9a96282dd53 Wed Apr 3 14:13:00 2019 -0700
    add link to trackDb definition document help refs #18869
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 1, context: html, text, full: html, text
    fff086f0ce7a549b800ec5ce3409a48287bd6732 Wed Apr 3 12:14:13 2019 -0700
    Updating the MANE track html description #23113
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 52, context: html, text, full: html, text
    fff086f0ce7a549b800ec5ce3409a48287bd6732 Wed Apr 3 12:14:13 2019 -0700
    Updating the MANE track html description #23113
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    fff086f0ce7a549b800ec5ce3409a48287bd6732 Wed Apr 3 12:14:13 2019 -0700
    Updating the MANE track html description #23113
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 24, context: html, text, full: html, text
    fe3d94f9b4c05194f24c081e138b32e6f3274792 Mon Apr 1 17:07:30 2019 -0700
    Adding rsync examples for querying the hgdownload-euro server, refs #20551
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 1, context: html, text, full: html, text
    fff086f0ce7a549b800ec5ce3409a48287bd6732 Wed Apr 3 12:14:13 2019 -0700
    Updating the MANE track html description #23113
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 18, context: html, text, full: html, text
    4ac85cdd8e240f9ad7d07d4a72c9b61ad9f2d21c Fri Apr 5 15:58:08 2019 -0700
    Adding VM20 release to newsarch & indexNews, refs #22997
  • lines changed 5, context: html, text, full: html, text
    746ef72bc9c7927689c5a84c2c96834240b2e99d Mon Apr 8 08:53:16 2019 -0700
    editing news arch for Gencode VM20, refs #22997
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    4ac85cdd8e240f9ad7d07d4a72c9b61ad9f2d21c Fri Apr 5 15:58:08 2019 -0700
    Adding VM20 release to newsarch & indexNews, refs #22997
• src/hg/htdocs/training/index.html
  • lines changed 31, context: html, text, full: html, text
    d375d1ccf52ce1b758cf6969196a18fcd6461183 Thu Mar 28 14:13:17 2019 -0700
    dropping completed singapore workshop. adding link to flyer for puerto rico. moved moscow course into upper list with dates.
  • lines changed 20, context: html, text, full: html, text
    130bca11796401b7e90bd910962e7825e775678c Sat Apr 6 04:36:52 2019 -0700
    dropped completed Costa Rica, added Guadalajara, made some listings more consistent format
• src/hg/hubApi/apiUtils.c
  • lines changed 23, context: html, text, full: html, text
    75af658048fd25b17153e6fff08712e48f78f61a Thu Apr 4 10:19:55 2019 -0700
    begin to think about error code returns refs #18869
  • lines changed 104, context: html, text, full: html, text
    dbd8fef5786457ba53375f006c4eaedf3d256110 Fri Apr 5 11:46:55 2019 -0700
    now output correct string or number json types refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 15, context: html, text, full: html, text
    dbd8fef5786457ba53375f006c4eaedf3d256110 Fri Apr 5 11:46:55 2019 -0700
    now output correct string or number json types refs #18869
• src/hg/hubApi/getData.c
  • lines changed 9, context: html, text, full: html, text
    a865b66cfeec6dea62ccdcd5a22c69e9a27335b6 Wed Apr 3 12:01:04 2019 -0700
    using new browser styles and allow genePred to print refs #18869
  • lines changed 98, context: html, text, full: html, text
    dbd8fef5786457ba53375f006c4eaedf3d256110 Fri Apr 5 11:46:55 2019 -0700
    now output correct string or number json types refs #18869
  • lines changed 19, context: html, text, full: html, text
    ff9f972ed500ac73b7d172766aa00b600438ad42 Fri Apr 5 23:50:14 2019 -0700
    fixup itemRgb column type for bigBed 9+ types refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 5, context: html, text, full: html, text
    7c72374b20a447962b0d2e302feceb27e371e10b Mon Apr 1 14:28:05 2019 -0700
    now using official help page refs #18869
  • lines changed 132, context: html, text, full: html, text
    97bf8f3cb8cbc74dcbe44625654ddf4af6b6e976 Tue Apr 2 13:18:05 2019 -0700
    calling bottleneck earlier in the game refs 18869
  • lines changed 54, context: html, text, full: html, text
    a865b66cfeec6dea62ccdcd5a22c69e9a27335b6 Wed Apr 3 12:01:04 2019 -0700
    using new browser styles and allow genePred to print refs #18869
  • lines changed 1, context: html, text, full: html, text
    824fca1285a93b3421bb9079c52779a61b2647e1 Wed Apr 3 12:54:55 2019 -0700
    remove stray line refs #18869
  • lines changed 10, context: html, text, full: html, text
    dbd8fef5786457ba53375f006c4eaedf3d256110 Fri Apr 5 11:46:55 2019 -0700
    now output correct string or number json types refs #18869
  • lines changed 78, context: html, text, full: html, text
    6103cfb97b45dafba47eced8573b21179823a63e Fri Apr 5 15:49:35 2019 -0700
    better html output refs #18869
• src/hg/hubApi/list.c
  • lines changed 6, context: html, text, full: html, text
    dbd8fef5786457ba53375f006c4eaedf3d256110 Fri Apr 5 11:46:55 2019 -0700
    now output correct string or number json types refs #18869
  • lines changed 2, context: html, text, full: html, text
    4f30cbd46d2beb5700bcb43f08ff00eb950876b0 Fri Apr 5 14:43:16 2019 -0700
    test checking
  • lines changed 2, context: html, text, full: html, text
    6103cfb97b45dafba47eced8573b21179823a63e Fri Apr 5 15:49:35 2019 -0700
    better html output refs #18869
• src/hg/hubApi/tests/expected/test10.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test11.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test12.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test13.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test14.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test15.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test16.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test19.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test8.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/expected/test9.gz
  • lines changed 0, context: html, text, full: html, text
    8168cdc271cc25c1dd5bc1038861a9d23a5be252 Fri Apr 5 11:52:49 2019 -0700
    updated test outputs now with correct JSON data types refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
  • lines changed 2, context: html, text, full: html, text
    7c72374b20a447962b0d2e302feceb27e371e10b Mon Apr 1 14:28:05 2019 -0700
    now using official help page refs #18869
• src/hg/inc/jksql.h
  • lines changed 28, context: html, text, full: html, text
    7c459941c1e589297e0014bf7957599f70836096 Thu Apr 4 11:08:18 2019 -0700
    moving some SQL functions to jksql.c from hgTables refs #18869 #23233
• src/hg/inc/lollipop.h
  • lines changed 0, context: html, text, full: html, text
    ae8dc8ab5e2c121398f31531c701ea064fb19aeb Thu Apr 4 07:05:40 2019 -0700
    add the ability to search the MANE track
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
  • lines changed 1, context: html, text, full: html, text
    a74afbfcfe01da0f925d8ff976cf5f2f13ce967d Sat Apr 6 16:23:21 2019 -0700
    more lolly work
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5a88f873d6dcc86b01809fb805f84532c93b38af Mon Apr 8 10:06:52 2019 -0700
    New version number v380
• src/hg/lib/customFactory.c
  • lines changed 16, context: html, text, full: html, text
    f12825443a141899e3b713a08b759377c0d8bcbf Thu Apr 4 13:51:53 2019 -0700
    Prevent segv when a vcfTabix custom track is specified with type=vcf instead. refs #23248 When type=vcf, we expect uncompressed VCF data to follow. But when a track line has type=vcf and no data after that, cpp->fileStack is popped to NULL while we're looking for header lines. So, check for NULL, and if we see the use of bigDataUrl, add a suggestion to use vcfTabix.
• src/hg/lib/hui.c
  • lines changed 53, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
  • lines changed 24, context: html, text, full: html, text
    d3875e2d3ebe45f89214d98a2c766a3771e7b057 Sun Apr 7 15:05:54 2019 -0700
    add manual view limits to lolly
  • lines changed 1, context: html, text, full: html, text
    b973bf71d1f2ed60125517f6fa69923a6faca7fa Sun Apr 7 15:55:16 2019 -0700
    add bigBed filtering to bigLolly
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    0efca62ffe8a10f6ce2141b2d7e7c66e4c69537c Wed Apr 3 14:01:47 2019 -0700
    Code review (thx Braney): didn't need to change errAbort to sqlAbort, change it back. refs #23184
  • lines changed 72, context: html, text, full: html, text
    7c459941c1e589297e0014bf7957599f70836096 Thu Apr 4 11:08:18 2019 -0700
    moving some SQL functions to jksql.c from hgTables refs #18869 #23233
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    1291f2242d9627684efaa88259c1c09f5e7c1b10 Thu Apr 4 07:19:11 2019 -0700
    some lollipop code leaked out on my last commit, so here's more leakage!
• src/hg/lib/vcfUi.c
  • lines changed 5, context: html, text, full: html, text
    489d28b9339f6b3cfa867d19a2855f2808205795 Fri Apr 5 09:52:55 2019 -0700
    vcfUi did not support track hubs -- it assumed it would be able to make a sql conn. Look for bigDataUrl first. refs #23252
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/filterTop.py
  • lines changed 66, context: html, text, full: html, text
    fe021d1df2f6a3e4cce72d28d97f54f0642900a3 Wed Apr 3 17:20:30 2019 -0700
    Changes to matrix filter script after code review, refs #23104
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    d8f3522539d953a90221e694c20a65204cfd1c5c Thu Apr 4 14:31:16 2019 -0700
    Fixing variable name typo
• src/hg/logCrawl/dbTrackAndSearchUsage/coocurrenceCounts/hg19Defaults.txt
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    fe021d1df2f6a3e4cce72d28d97f54f0642900a3 Wed Apr 3 17:20:30 2019 -0700
    Changes to matrix filter script after code review, refs #23104
• src/hg/makeDb/doc/encode3/tfbs.txt
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
    Add scripts and make docs for ENCODE 3 TF binding site tracks. refs #21139
• src/hg/makeDb/doc/encodeRegHg19.txt
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
    Add scripts and make docs for ENCODE 3 TF binding site tracks. refs #21139
• src/hg/makeDb/doc/hg38/mane.txt
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    ae8dc8ab5e2c121398f31531c701ea064fb19aeb Thu Apr 4 07:05:40 2019 -0700
    add the ability to search the MANE track
• src/hg/makeDb/doc/mm10.txt
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    3846c108e2ff699c4d1de31c4b38f7379e1cf9ee Sat Apr 6 07:51:15 2019 -0700
    new CDS FASTA downloads in honor of Gencode VM20 release
• src/hg/makeDb/hgBedsToBedExps/bedExpsToFactorSource.pl
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    f464e85e868ff6c5ef8d97c24cb990078a8fd723 Wed Apr 3 11:28:55 2019 -0700
    Tools for factorSource format. refs #21139
• src/hg/makeDb/hgBedsToBedExps/factorSourceCheckScore.pl
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    f464e85e868ff6c5ef8d97c24cb990078a8fd723 Wed Apr 3 11:28:55 2019 -0700
    Tools for factorSource format. refs #21139
• src/hg/makeDb/outside/encode3/tfbs/dac_dec2018/README.txt
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
    Add scripts and make docs for ENCODE 3 TF binding site tracks. refs #21139
• src/hg/makeDb/outside/encode3/tfbs/dac_dec2018/makeFilelist.pl
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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• src/hg/makeDb/outside/encode3/tfbs/dac_dec2018/makeInputs.pl
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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• src/hg/makeDb/outside/encode3/tfbs/dac_dec2018/makeTrackDb.pl
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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• src/hg/makeDb/trackDb/human/encode3RegTfbsCluster.html
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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• src/hg/makeDb/trackDb/human/hg19/encode3.ra
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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    3f6f7810a3a55c96f40b38fee3e7574fe2d016c0 Wed Apr 3 14:45:50 2019 -0700
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    702027afdbe700e69a3f553baf1e0341aad2bd27 Thu Apr 4 14:23:17 2019 -0700
    Fix handling of release tag (make tdbQuery -release=beta happy)
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    ad7467196611835c90cc7eed12dbcf973fc6a7ae Thu Apr 4 14:26:49 2019 -0700
    Remove debug tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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    702027afdbe700e69a3f553baf1e0341aad2bd27 Thu Apr 4 14:23:17 2019 -0700
    Fix handling of release tag (make tdbQuery -release=beta happy)
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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    ee7b1156b945e6a7768a20128926c13b9c18e040 Wed Apr 3 12:16:23 2019 -0700
    Add defaults (a few arbitrary) to composite. refs #23243
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    3f6f7810a3a55c96f40b38fee3e7574fe2d016c0 Wed Apr 3 14:45:50 2019 -0700
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    702027afdbe700e69a3f553baf1e0341aad2bd27 Thu Apr 4 14:23:17 2019 -0700
    Fix handling of release tag (make tdbQuery -release=beta happy)
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    ad7467196611835c90cc7eed12dbcf973fc6a7ae Thu Apr 4 14:26:49 2019 -0700
    Remove debug tracks. refs #21139
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
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    e447af61b34836fb33b1be5d28979810696bbf71 Fri Apr 5 12:02:50 2019 -0700
    trackDb for GDC Cancer track
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    917be30f5ffa9ae50da1d8d42a3935b5a4bf1105 Sun Apr 7 15:56:30 2019 -0700
    bigBed filtering for gdcCancer track
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    03844649e7c49bfd2fbe2f1918cdb4dac92c8700 Sun Apr 7 16:52:38 2019 -0700
    fix gdcCancer filter values
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    570d8afd51d864e1875d9fa4a93c26ab061e8da4 Sun Apr 7 17:09:23 2019 -0700
    oops, need the full cancer names for the gdc projects
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    2db80a766abaf970960c4dbe127b5cb346bbdc52 Mon Apr 1 14:21:36 2019 -0700
    Improving GENCODE html ref#23170
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    0572de882d6728903b0d75ba1a7a57eee1ef7e67 Tue Apr 2 11:11:34 2019 -0700
    Improvements to knownGene page ref#23170
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    ebf7df5e805ec29fa7f21cc99a7a815f2141fb7a Wed Apr 3 11:31:01 2019 -0700
    Sprucing up the knownGenes page ref#23170
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    675edeebadc7768baf3af64add519dfee2dafcf1 Wed Apr 3 12:38:09 2019 -0700
    Making a small correction on knownGene html ref#23170
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    6607c540cea82fb6c92358a4f214b77a0dffcc1b Thu Apr 4 10:23:15 2019 -0700
    Touching up knownGene.html ref#23170
• src/hg/makeDb/trackDb/human/hg38/mane.html
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    fff086f0ce7a549b800ec5ce3409a48287bd6732 Wed Apr 3 12:14:13 2019 -0700
    Updating the MANE track html description #23113
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    e06833b346cc6b30dd8bf11ad075a94c42103cc6 Wed Apr 3 12:20:38 2019 -0700
    Updating MANE links #23113
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    1eeca67bba9c9bbb0b3ed49ac5bcb47c0d3e19f4 Wed Apr 3 14:44:10 2019 -0700
    Adding the note from MANE authors.
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    7b257c40c81ea80d93454fe09aec114d6921ecb1 Fri Apr 5 14:49:39 2019 -0700
    Encoding emails for bot protection #23113
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    ae8dc8ab5e2c121398f31531c701ea064fb19aeb Thu Apr 4 07:05:40 2019 -0700
    add the ability to search the MANE track
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    d87e5f63bc000d560c21bca638b6d5f3dee0173d Wed Apr 3 12:06:45 2019 -0700
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    702027afdbe700e69a3f553baf1e0341aad2bd27 Thu Apr 4 14:23:17 2019 -0700
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    e447af61b34836fb33b1be5d28979810696bbf71 Fri Apr 5 12:02:50 2019 -0700
    trackDb for GDC Cancer track
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.alpha.ra
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    2109d64d4013e37dd4be158d6fba17235269a421 Thu Apr 4 16:11:45 2019 -0700
    Adding knownGene description page to VM20 for mm10, refs #22997
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
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    2109d64d4013e37dd4be158d6fba17235269a421 Thu Apr 4 16:11:45 2019 -0700
    Adding knownGene description page to VM20 for mm10, refs #22997
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.ra
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    2109d64d4013e37dd4be158d6fba17235269a421 Thu Apr 4 16:11:45 2019 -0700
    Adding knownGene description page to VM20 for mm10, refs #22997
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
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    b90e71d3ddbb844051b0df05308526bbf9cd7717 Fri Apr 5 13:29:28 2019 -0700
    Updating Tabula Muris splice site shortLabels since four cell types had the same name, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    c3581ce33c07f06734b06cabee0f1e1e231d468a Wed Apr 3 08:18:36 2019 -0700
    Removing beta release tags from knownGene, refs #22997
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    2109d64d4013e37dd4be158d6fba17235269a421 Thu Apr 4 16:11:45 2019 -0700
    Adding knownGene description page to VM20 for mm10, refs #22997
• src/hg/makeDb/trackDb/tagTypes.tab
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    24369c1be94e4ba70b021ef003e313fb01aac843 Thu Apr 4 10:56:50 2019 -0700
    some lollipop things
• src/hg/makefile
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    15dd09132bccb9880a64a3cac422d23e1abd0674 Mon Apr 8 09:51:26 2019 -0700
    adding hubApi to the CGI build refs #18869
• src/inc/srcVersion.h
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    5a88f873d6dcc86b01809fb805f84532c93b38af Mon Apr 8 10:06:52 2019 -0700
    New version number v380
• src/utils/cancerMafToBigBed
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    7ec55fe7a016d7da941602e441ed242a8e241b24 Mon Apr 8 07:59:45 2019 -0700
    usage update to the maf converter, no redmine
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
    Letting python handle printing of floats instead of custom float parser, also allowing fix or alt sequences, refs #23218
• src/utils/expMatrixToBarchartBed/tests/floats.coords
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
    Letting python handle printing of floats instead of custom float parser, also allowing fix or alt sequences, refs #23218
• src/utils/expMatrixToBarchartBed/tests/floats.matrix
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
    Letting python handle printing of floats instead of custom float parser, also allowing fix or alt sequences, refs #23218
• src/utils/expMatrixToBarchartBed/tests/floats.meta
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
    Letting python handle printing of floats instead of custom float parser, also allowing fix or alt sequences, refs #23218
• src/utils/expMatrixToBarchartBed/tests/floats.output
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
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• src/utils/expMatrixToBarchartBed/tests/makefile
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    e86711604cdb883a23ee8af668b49e4d666dae5c Tue Apr 2 13:58:55 2019 -0700
    Letting python handle printing of floats instead of custom float parser, also allowing fix or alt sequences, refs #23218
• src/utils/git-reports/git-reports.c
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    54f9a7c7d96dc31d61296038bcad4a9a041ef3ea Fri Apr 5 09:16:31 2019 -0700
    adding to the no diff message that it can also be caused by a change of file-permissions
• src/utils/qa/runJoiner.csh
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    f5c601799ce10f33e75e5a81969b537072a3c123 Thu Mar 14 13:45:49 2019 -0700
    added a line of output soyou know which identifier is being run
• src/utils/qa/weeklybld/buildEnv.csh
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    b98b7d724fa236487f7d27cf1a972222860bf5f3 Mon Apr 8 10:05:32 2019 -0700
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