All File Changes

v380_preview to v380_preview2 (2019-03-25 to 2019-04-01) v380

• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
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    638bb4dbb5df4c892c18759d23217f9e6af2d730 Wed Mar 13 12:12:16 2019 -0700
    Adding some missing newlines to status message.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 4, context: html, text, full: html, text
    5c2dea36479f0669a316e693c21a375d192b9e38 Wed Mar 13 12:13:20 2019 -0700
    Making cdwPairedEnd basically ignore 10x files by allowing new paired_end values cell_barcode and sample_barcode instead of 1 2.
• src/hg/cirm/cdw/lib/cdwPageFooter.h
  • lines changed 0, context: html, text, full: html, text
    e35c51bccf99015d94ca90d91cce47da59b6a995 Tue Mar 26 23:01:56 2019 -0700
    file perms .h file should not be executable
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    48df2023b146ce66aeb8dc837bf7f19970f0c01a Wed Mar 27 14:53:47 2019 -0700
    adding comments that these header and footer files in gateway/htdocs/inc/ and cdw/lib/ need to stay in sync when making modifications
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 1, context: html, text, full: html, text
    258a5fadc1e73e5a7d16b4618e9130f69545fb82 Tue Mar 26 15:20:46 2019 -0700
    Renamed top-level menu element Files to Data. refs#23075
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    48df2023b146ce66aeb8dc837bf7f19970f0c01a Wed Mar 27 14:53:47 2019 -0700
    adding comments that these header and footer files in gateway/htdocs/inc/ and cdw/lib/ need to stay in sync when making modifications
• src/hg/cirm/cdw/oneShot/checkSymlinkTargetType/checkSymlinkTargetType.c
  • lines changed 3, context: html, text, full: html, text
    de2a8da6f2feec44751df56de592b196bbae458f Tue Mar 26 15:51:31 2019 -0700
    small improvements
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 1, context: html, text, full: html, text
    48df2023b146ce66aeb8dc837bf7f19970f0c01a Wed Mar 27 14:53:47 2019 -0700
    adding comments that these header and footer files in gateway/htdocs/inc/ and cdw/lib/ need to stay in sync when making modifications
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 1, context: html, text, full: html, text
    258a5fadc1e73e5a7d16b4618e9130f69545fb82 Tue Mar 26 15:20:46 2019 -0700
    Renamed top-level menu element Files to Data. refs#23075
  • lines changed 2, context: html, text, full: html, text
    b0a954a28830c0bca0a8ff56897823c0bc9513a3 Wed Mar 27 00:47:08 2019 -0700
    Changing to suppress login top menu links on public cirm. refs#22949
  • lines changed 1, context: html, text, full: html, text
    48df2023b146ce66aeb8dc837bf7f19970f0c01a Wed Mar 27 14:53:47 2019 -0700
    adding comments that these header and footer files in gateway/htdocs/inc/ and cdw/lib/ need to stay in sync when making modifications
• src/hg/cirm/gateway/htdocs/js/cirmStuff.js
  • lines changed 4, context: html, text, full: html, text
    b0a954a28830c0bca0a8ff56897823c0bc9513a3 Wed Mar 27 00:47:08 2019 -0700
    Changing to suppress login top menu links on public cirm. refs#22949
• src/hg/cirm/gateway/index-obsolete.php
  • lines changed 1283, context: html, text, full: html, text
    8860fd4a6aebcd8e94c19e204041e83d4cc80448 Tue Mar 26 22:29:48 2019 -0700
    Want to make sure no one tries to use this anymore.
• src/hg/cirm/gateway/index.php
  • lines changed 1283, context: html, text, full: html, text
    8860fd4a6aebcd8e94c19e204041e83d4cc80448 Tue Mar 26 22:29:48 2019 -0700
    Want to make sure no one tries to use this anymore.
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    296345a5b609ce441cc32982d4bde521c76c09d5 Wed Mar 27 04:09:01 2019 -0700
    fixing hgLogin bug, this is the minimal change to fix the bug, refs #23202
  • lines changed 9, context: html, text, full: html, text
    92353af6dbfaf9764380a0d1e1219428cc4f942e Wed Mar 27 04:10:25 2019 -0700
    fixing hgLogin bug, this is an extended bugfix that improves the logic, the email-send function is now not redirecting anymore, refs #23202
  • lines changed 2, context: html, text, full: html, text
    95aceeb7d6ed6e2b686fff6149663a226c099bb4 Wed Mar 27 04:30:49 2019 -0700
    adding spam folder message to hglogin email sent message, refs #21378
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 1, context: html, text, full: html, text
    00747350bbebd0a84c7e3fd504ca5cc74124862c Wed Mar 27 10:32:42 2019 -0700
    Closing forgotten <tr> anchor for CR ref#23188
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 74, context: html, text, full: html, text
    80288e7ecadb017ea194cfcbfeb022cee8b17e7f Fri Mar 29 08:19:30 2019 -0700
    beginning JSON API documentation refs #18869
  • lines changed 100, context: html, text, full: html, text
    ef83c5a7e3bb6168a91478e1b7be4318d7578a1a Fri Mar 29 11:11:39 2019 -0700
    adding example URLs refs #18869
  • lines changed 61, context: html, text, full: html, text
    9960cf0397087eb029ab212ff7d0b9fdcdc94c87 Fri Mar 29 15:11:56 2019 -0700
    now with a full set of examples refs #18869
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    c5a8cc19a265ee00e2cef1fcdb0d6693dd6d6bc3 Wed Mar 27 11:09:42 2019 -0700
    Editing newarch.html to fix HTML entities, refs #23190
• src/hg/htdocs/style/jquery.treetable.css
  • lines changed 0, context: html, text, full: html, text
    9f33f5f0ce2743e5fb50cda22dd4c45f3fa09f3d Fri Mar 29 15:50:35 2019 -0700
    fixing silly perm problem
• src/hg/hubApi/apiUtils.c
  • lines changed 3, context: html, text, full: html, text
    136481ed08005073b11b1b1f326ee7c85f4d2f58 Tue Mar 26 13:14:56 2019 -0700
    adding the botDelay functions refs #18869
  • lines changed 53, context: html, text, full: html, text
    3bbad1670f2e44ca41d06c657b8f8636abfce4fb Wed Mar 27 14:47:11 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    136481ed08005073b11b1b1f326ee7c85f4d2f58 Tue Mar 26 13:14:56 2019 -0700
    adding the botDelay functions refs #18869
  • lines changed 9, context: html, text, full: html, text
    3bbad1670f2e44ca41d06c657b8f8636abfce4fb Wed Mar 27 14:47:11 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/getData.c
  • lines changed 2, context: html, text, full: html, text
    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
  • lines changed 3, context: html, text, full: html, text
    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
  • lines changed 42, context: html, text, full: html, text
    3bbad1670f2e44ca41d06c657b8f8636abfce4fb Wed Mar 27 14:47:11 2019 -0700
    provide list chrom function for hubs refs #18869
  • lines changed 2, context: html, text, full: html, text
    8d6e9ae8ab451313eabf7f6c87d9435eedf702ac Fri Mar 29 11:13:19 2019 -0700
    add chrom print out to track getData and fix up test harness to be more general refs #18869
  • lines changed 96, context: html, text, full: html, text
    1bfad89c514f15aef219d6bfdcca6f9f754c3ac8 Fri Mar 29 15:13:56 2019 -0700
    now returning DNA sequence from assembly or track hub refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 52, context: html, text, full: html, text
    136481ed08005073b11b1b1f326ee7c85f4d2f58 Tue Mar 26 13:14:56 2019 -0700
    adding the botDelay functions refs #18869
  • lines changed 1, context: html, text, full: html, text
    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
  • lines changed 31, context: html, text, full: html, text
    3bbad1670f2e44ca41d06c657b8f8636abfce4fb Wed Mar 27 14:47:11 2019 -0700
    provide list chrom function for hubs refs #18869
  • lines changed 1, context: html, text, full: html, text
    1bfad89c514f15aef219d6bfdcca6f9f754c3ac8 Fri Mar 29 15:13:56 2019 -0700
    now returning DNA sequence from assembly or track hub refs #18869
• src/hg/hubApi/list.c
  • lines changed 2, context: html, text, full: html, text
    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
  • lines changed 149, context: html, text, full: html, text
    3bbad1670f2e44ca41d06c657b8f8636abfce4fb Wed Mar 27 14:47:11 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/makefile
  • lines changed 5, context: html, text, full: html, text
    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected.json.gz
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    99053ad4db25a38b8e290235a2e15b325e2e568a Tue Mar 26 20:14:00 2019 -0700
    test result no longer needed refs #18869
• src/hg/hubApi/tests/expected/test0.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    88bfbff010507fe4327e1d3f51feb5c811d5b97f Fri Mar 29 11:14:04 2019 -0700
    now running test0 explicitly with argument refs #18869
• src/hg/hubApi/tests/expected/test1.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test10.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    5bc5745e2cc4a0e729b2d97ccd24bc74390d1a7c Fri Mar 29 15:17:14 2019 -0700
    now testing DNA sequence return from assembly and track hubs refs #18869
• src/hg/hubApi/tests/expected/test11.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test12.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test13.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test14.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test15.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test16.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test17.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test18.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
• src/hg/hubApi/tests/expected/test19.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
• src/hg/hubApi/tests/expected/test2.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test20.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test21.gz
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
• src/hg/hubApi/tests/expected/test22.gz
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test23.gz
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test24.gz
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    e4bdd0d12972eda9b31a90bba71236dc6a4491bc Fri Mar 29 15:49:48 2019 -0700
    adding test24 and test25 DNA sequence from assembly and track hub refs #18869
• src/hg/hubApi/tests/expected/test25.gz
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    e4bdd0d12972eda9b31a90bba71236dc6a4491bc Fri Mar 29 15:49:48 2019 -0700
    adding test24 and test25 DNA sequence from assembly and track hub refs #18869
• src/hg/hubApi/tests/expected/test3.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test4.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test5.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
• src/hg/hubApi/tests/expected/test6.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test7.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
• src/hg/hubApi/tests/expected/test8.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
• src/hg/hubApi/tests/expected/test9.gz
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    5bc5745e2cc4a0e729b2d97ccd24bc74390d1a7c Fri Mar 29 15:17:14 2019 -0700
    now testing DNA sequence return from assembly and track hubs refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    fc452e9c75747702a8a312d7943b3607f8328158 Wed Mar 27 14:58:11 2019 -0700
    adding /list/chromosomes function for hubs refs #18869
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    8d6e9ae8ab451313eabf7f6c87d9435eedf702ac Fri Mar 29 11:13:19 2019 -0700
    add chrom print out to track getData and fix up test harness to be more general refs #18869
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    5bc5745e2cc4a0e729b2d97ccd24bc74390d1a7c Fri Mar 29 15:17:14 2019 -0700
    now testing DNA sequence return from assembly and track hubs refs #18869
• src/hg/hubApi/tests/makefile
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    e1ace7526b7d16654717065227a2d1e6f3fe4654 Tue Mar 26 20:12:20 2019 -0700
    adding testing for hubApi refs #18869
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    0edb8745a4b8d2f2e5558d592515fde615786a90 Tue Mar 26 20:20:11 2019 -0700
    need to make the testOutput directory to get started refs #18869
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    dd184bbf868ed714e3d536d5eacbd19645bb1f63 Wed Mar 27 09:39:33 2019 -0700
    output the track name and sqlTable name if different refs #18869
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    51db0a5d14bdc077c2092dc632b57c17d09d0404 Wed Mar 27 14:49:28 2019 -0700
    provide list chrom function for hubs refs #18869
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    8d6e9ae8ab451313eabf7f6c87d9435eedf702ac Fri Mar 29 11:13:19 2019 -0700
    add chrom print out to track getData and fix up test harness to be more general refs #18869
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    5bc5745e2cc4a0e729b2d97ccd24bc74390d1a7c Fri Mar 29 15:17:14 2019 -0700
    now testing DNA sequence return from assembly and track hubs refs #18869
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    e4bdd0d12972eda9b31a90bba71236dc6a4491bc Fri Mar 29 15:49:48 2019 -0700
    adding test24 and test25 DNA sequence from assembly and track hub refs #18869
• src/hg/js/jquery.treetable.js
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    d72a8b0821e007be662450f3a4809ae556e8618d Wed Mar 27 23:54:17 2019 -0700
    removing unneeded and pointlessly different exec perms on jquery.treetable.js
• src/hg/makeDb/trackDb/chicken/galGal6/chainNet.html
  • lines changed 178, context: html, text, full: html, text
    edc3b70da9383b7c7aa62fa66341ec7dc89e60ea Mon Mar 25 13:51:46 2019 -0700
    correct html page for the chainNet composites refs #22687
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetBirds.ra
  • lines changed 2, context: html, text, full: html, text
    edc3b70da9383b7c7aa62fa66341ec7dc89e60ea Mon Mar 25 13:51:46 2019 -0700
    correct html page for the chainNet composites refs #22687
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetFish.ra
  • lines changed 2, context: html, text, full: html, text
    edc3b70da9383b7c7aa62fa66341ec7dc89e60ea Mon Mar 25 13:51:46 2019 -0700
    correct html page for the chainNet composites refs #22687
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetvertebrate.ra
  • lines changed 2, context: html, text, full: html, text
    edc3b70da9383b7c7aa62fa66341ec7dc89e60ea Mon Mar 25 13:51:46 2019 -0700
    correct html page for the chainNet composites refs #22687
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.77way.ra
  • lines changed 1, context: html, text, full: html, text
    ebf7fd00e599e72aeb386c3a762cae8d10e5376e Mon Apr 1 09:04:53 2019 -0700
    Removing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    e69fc29618110aade3a9f913843d8cb994419f9e Thu Mar 28 09:52:39 2019 -0700
    Updating http to https for braFlo1, uiLinks cronjob.
• src/hg/makeDb/trackDb/lancelet/braFlo1/phastConsElements5way.html
  • lines changed 5, context: html, text, full: html, text
    e69fc29618110aade3a9f913843d8cb994419f9e Thu Mar 28 09:52:39 2019 -0700
    Updating http to https for braFlo1, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/GRCm38B/trackDb.ra
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    bc4683f0dd30eb61238cb80d12ccaa040ae0aee5 Fri Mar 29 15:44:03 2019 -0700
    added track for GENCODE/GRCm38B evaulation
  • lines changed 25, context: html, text, full: html, text
    bdae9c57c543f8faa986773e2afe0dc409ecff04 Sat Mar 30 06:05:55 2019 -0700
    added gencode VM20 BLAT track to GRCm38B
• src/hg/makefile
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    9970daa5fc0415f812953f39dfc49a8503c78588 Wed Mar 27 23:46:06 2019 -0700
    removing redundant clause in cgi target of makefile
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    a743575c79c1370bf4d7ad9573649bbc42e017a0 Mon Mar 25 11:23:38 2019 -0700
    version 43. put the connection back like it was. doubled the timeout. incremented version.
• src/inc/common.mk
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    ccc9f64c81d44f2e734c61cc73149f60e7768b10 Tue Mar 26 19:16:36 2019 -0700
    required new library on Mac OSX refs #23070
• src/utils/qa/weeklybld/buildEnv.csh
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    c53b91d7a2c0986df7872b2af76abb38af95035a Mon Apr 1 11:36:03 2019 -0700
    v380 preview2, refs #23203

• lines changed: 4043
• files changed: 106