All File Changes

v381_base to v382_preview (2019-04-29 to 2019-05-06) v382

• confs/hgwdev.hg.conf
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    8a6f187e8a8a02d0f8d8f07b4ed0a6d88756af37 Sun May 5 01:11:48 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 14, context: html, text, full: html, text
    ce40b81bba5b53d95c9152d6d769cf44295ac5e6 Mon Apr 29 14:33:25 2019 -0700
    Moving Research Theme/Lab/Dataset header down in table, refs #23132
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 1, context: html, text, full: html, text
    99a383130c566240bc9ab5b3dffaf2c939a11c10 Mon Apr 29 14:30:57 2019 -0700
    adding external link icon for cell browser website
• src/hg/hgBlat/hgBlat.c
  • lines changed 20, context: html, text, full: html, text
    d23aa1e7bfa38c3cb266decd97e8878713872a91 Tue Apr 30 14:29:27 2019 -0700
    changing wording of "all genomes" BLAT docs, green lighted by Brian Lee, no redmine
  • lines changed 3, context: html, text, full: html, text
    88483f54e928d2341e942d5f617ea935b8e5dbf4 Wed May 1 13:06:59 2019 -0700
    Small improvement in hgBlat All Genomes output explanation in the header.
  • lines changed 1, context: html, text, full: html, text
    fb8ab3a8c2837b5d25d8b24da2870f0f9cdf928d Wed May 1 15:43:00 2019 -0700
    Improving hgBlat No Matches found output.
  • lines changed 2, context: html, text, full: html, text
    bb56ceb3db06320c7bf4ba6e5f1e14b88b51afac Thu May 2 01:43:25 2019 -0700
    adding link to BLAT faq to blat all output, refs #23441
  • lines changed 2, context: html, text, full: html, text
    a9947a9b812bb9ac68e6758a7976e00dae5f3aec Thu May 2 14:46:13 2019 -0700
    Further improving hgBlat blat all genomes explanation.
  • lines changed 3, context: html, text, full: html, text
    0690b4ca888dc702e80b96144c6977082b101efe Thu May 2 14:53:53 2019 -0700
    finish merge conflict, polished text a little.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    35eb90236a20e79c4f4e80a9d0cf8615ee85b80e Wed May 1 10:43:53 2019 -0700
    Fixing typo noticed by code review, refs #23397
• src/hg/hgSession/sessionData.c
  • lines changed 7, context: html, text, full: html, text
    a8c88d64b3a8adf8d6b522247b89c327b36e2a66 Mon Apr 29 10:41:21 2019 -0700
    Don't create new userdata directory unless we have at least one file to store there. Thx Hiram
• src/hg/hgTracks/lollyTrack.c
  • lines changed 11, context: html, text, full: html, text
    853a2deb64b72bb0ad5b85128f598925e815ee5b Tue Apr 30 15:33:37 2019 -0700
    don't put out more than 5,000 map boxes because more than that freaks out Chrome
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    63a3a58e1bfce5a0a8b44cb7b5f76d0c3c6b64a9 Fri May 3 11:18:58 2019 -0700
    don't free memory that we didn't allocate
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 36, context: html, text, full: html, text
    a2c7461148241e1514b1522aa60a200faaed24ed Wed May 1 14:22:54 2019 -0700
    Adding entry to BLAT FAQ explaining BLAT All hits #23411
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    b4ed5e2397d26437a76fee1360d2534668aac013 Fri May 3 13:42:10 2019 -0700
    Adding hgdownload-euro rsync and ftp examples, refs #20551
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 19, context: html, text, full: html, text
    b1dd32138ff6eb6a5ff7a9b55135abf3cd04bd69 Mon Apr 29 16:56:28 2019 -0700
    Various minor fixes for code review #23399, doc is still rough draft
  • lines changed 147, context: html, text, full: html, text
    c40254b52f058ca7662886a248738ac13c817a7d Thu May 2 17:06:00 2019 -0700
    minor changes to TOC, links, hgsid, and position #23131
  • lines changed 76, context: html, text, full: html, text
    26e75bcc08d44f024ac657e96ef829295411cb95 Fri May 3 14:35:41 2019 -0700
    Pushing changes including formatting, typo corrections, and composite track info #23131
  • lines changed 7, context: html, text, full: html, text
    5edfe0d443d3a5bcca48f79392f5e0ed8e9b457b Fri May 3 15:34:59 2019 -0700
    Adding questions to the sections #23131
  • lines changed 3, context: html, text, full: html, text
    da9bfb0be4cf7ad610abb4f1e8d082b286ec759b Fri May 3 16:19:25 2019 -0700
    Fixed typos #21313
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 105, context: html, text, full: html, text
    bf6b2d5aeaf8111cfd9782b265893c6f14072939 Mon Apr 29 13:40:03 2019 -0700
    Fixing some word flow/coding conventions on API help page ref#18869
  • lines changed 20, context: html, text, full: html, text
    37f6df9b99275b791d284eeac8d641e0cf2f9b41 Wed May 1 15:36:44 2019 -0700
    clean up HTML via W3C validator refs #18869
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 4, context: html, text, full: html, text
    89c380d28049d3f28fd09a897260d1ee0fbb3248 Mon Apr 29 15:32:09 2019 -0700
    Making upper case Browser for code review #23399
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 7, context: html, text, full: html, text
    b4ed5e2397d26437a76fee1360d2534668aac013 Fri May 3 13:42:10 2019 -0700
    Adding hgdownload-euro rsync and ftp examples, refs #20551
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    2c25c75b9637aa1884e7298695fa6015498eee52 Fri May 3 13:45:20 2019 -0700
    Changing 'UCSC Genome Bioinformatics' to 'UCSC Genome Browser', and changing 'site' to 'server', no Redmine.
  • lines changed 14, context: html, text, full: html, text
    b066b38ccaff9d15f82a8888ecec6c7267a8c067 Fri May 3 14:45:27 2019 -0700
    Using definition lists instead of <strong> tags, refs #20551
  • lines changed 28, context: html, text, full: html, text
    ae5fe3be649000cb4c68fe6bcf9401b8f8776baf Fri May 3 16:02:33 2019 -0700
    Adding rsync and FTP examples for hgdownload-euro, refs #20551
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 1, context: html, text, full: html, text
    6a1988273860acb652ac951a47562181560080a4 Mon Apr 29 16:13:23 2019 -0700
    Adding images to hgWiggleHelp.html, refs #23300
  • lines changed 65, context: html, text, full: html, text
    306adf30a9bd27675d597ac0ebc1c76ec653f737 Tue Apr 30 09:07:58 2019 -0700
    adding images and editing hgWiggletrackHelp.html, refs #23300
  • lines changed 73, context: html, text, full: html, text
    91bd83bd842d660b671257a4baefccd9e2e39b16 Thu May 2 15:09:21 2019 -0700
    adding images and rearrange text on hgWiggleTrackHelp.html, refs #23300
  • lines changed 3, context: html, text, full: html, text
    fd1449d98ffc991fb02795bc3a5388a83d1d2d98 Thu May 2 15:57:35 2019 -0700
    editing typo & moving images, refs #23300
  • lines changed 6, context: html, text, full: html, text
    cc108658460e00acfb5380658d844e82a1c72a1f Fri May 3 10:26:28 2019 -0700
    Adding negate values image & text to hgWiggle docs, refs #23300
  • lines changed 39, context: html, text, full: html, text
    8185d6095db9c89a6ca7c9003545f6b476998d57 Fri May 3 13:50:55 2019 -0700
    Changing <ul> to <dl> for the image sections of hgWiggle, refs #23396
  • lines changed 5, context: html, text, full: html, text
    4c58c151205aa0b874645607709bd42c822662ad Fri May 3 14:00:34 2019 -0700
    Editing images section text for hgWiggle, refs #23396
  • lines changed 1, context: html, text, full: html, text
    a4fcef6bb047274c0c49e2ced418852df7ccc893 Fri May 3 14:51:56 2019 -0700
    Editing typo on hgWiggle, refs #23300
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 4, context: html, text, full: html, text
    b4ed5e2397d26437a76fee1360d2534668aac013 Fri May 3 13:42:10 2019 -0700
    Adding hgdownload-euro rsync and ftp examples, refs #20551
• src/hg/htdocs/images/2conf_enco.png
  • lines changed 0, context: html, text, full: html, text
    91bd83bd842d660b671257a4baefccd9e2e39b16 Thu May 2 15:09:21 2019 -0700
    adding images and rearrange text on hgWiggleTrackHelp.html, refs #23300
• src/hg/htdocs/images/conf_enco.png
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    9f486c7d74f7fa0d13867e5a7d0820c6b75e1373 Tue Apr 30 09:10:36 2019 -0700
    adding additional image to hgWiggleTrackHelp.html, refs #23300
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    cfc7183ad88e402c8ce045c695fe4059aa6d2623 Thu May 2 15:45:46 2019 -0700
    removing unused images, refs #23300
• src/hg/htdocs/images/conf_encode.png
  • lines changed 0, context: html, text, full: html, text
    6a1988273860acb652ac951a47562181560080a4 Mon Apr 29 16:13:23 2019 -0700
    Adding images to hgWiggleHelp.html, refs #23300
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    cfc7183ad88e402c8ce045c695fe4059aa6d2623 Thu May 2 15:45:46 2019 -0700
    removing unused images, refs #23300
• src/hg/htdocs/images/encode_none-1.png
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    306adf30a9bd27675d597ac0ebc1c76ec653f737 Tue Apr 30 09:07:58 2019 -0700
    adding images and editing hgWiggletrackHelp.html, refs #23300
• src/hg/htdocs/images/encode_solid-1.png
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    306adf30a9bd27675d597ac0ebc1c76ec653f737 Tue Apr 30 09:07:58 2019 -0700
    adding images and editing hgWiggletrackHelp.html, refs #23300
• src/hg/htdocs/images/encode_stack-1.png
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    306adf30a9bd27675d597ac0ebc1c76ec653f737 Tue Apr 30 09:07:58 2019 -0700
    adding images and editing hgWiggletrackHelp.html, refs #23300
• src/hg/htdocs/images/trans_encode-1.png
  • lines changed 0, context: html, text, full: html, text
    306adf30a9bd27675d597ac0ebc1c76ec653f737 Tue Apr 30 09:07:58 2019 -0700
    adding images and editing hgWiggletrackHelp.html, refs #23300
• src/hg/htdocs/images/wig_negate-1.png
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    cc108658460e00acfb5380658d844e82a1c72a1f Fri May 3 10:26:28 2019 -0700
    Adding negate values image & text to hgWiggle docs, refs #23300
• src/hg/htdocs/images/wiggle_y-1.png
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    2fab6aa80de8fbfa9d33db84cd98006fee413d4f Tue Apr 30 09:22:39 2019 -0700
    adding image of y line to hgWiggle, refs #23300
• src/hg/hubApi/apiUtils.c
  • lines changed 54, context: html, text, full: html, text
    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 6, context: html, text, full: html, text
    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
  • lines changed 2, context: html, text, full: html, text
    6125c59026d71350da69c9e00bfabd43016b791a Wed May 1 14:47:00 2019 -0700
    add hg.conf variable to turn on the html output on the URL /cgi-bin/hubApi refs #18869
• src/hg/hubApi/getData.c
  • lines changed 13, context: html, text, full: html, text
    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
  • lines changed 1, context: html, text, full: html, text
    42d60420cb2b703a3cfe2134d6d7cf77f32cee8c Tue Apr 30 10:46:41 2019 -0700
    missing argument on apiErrAbort call, it results in a sigsegv refs #18869
  • lines changed 8, context: html, text, full: html, text
    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    9347e8dbe261da242e07497d64570bfe142b5930 Tue Apr 30 18:24:54 2019 -0700
    do not allow arbitrary garbage to get in via PATH_INFO refs #18869
  • lines changed 20, context: html, text, full: html, text
    183a7505b5251fb0bdc4a6fca6d6420ed6a8d4b7 Wed May 1 14:46:21 2019 -0700
    add hg.conf variable to turn on the html output on the URL /cgi-bin/hubApi refs #18869
  • lines changed 1, context: html, text, full: html, text
    a05ae5a901ce49be3ae8d4beb40308c65a16ef85 Wed May 1 15:28:51 2019 -0700
    correctly supply a Location header in the redirect refs #18869
  • lines changed 33, context: html, text, full: html, text
    3ce41962a262ede824372d486cf8da609f3d3ae3 Thu May 2 14:22:43 2019 -0700
    checking for multiple instances of arguments and illegal strings on jsonOutputArrays and trackLeavesOnly refs #18869
• src/hg/hubApi/list.c
  • lines changed 31, context: html, text, full: html, text
    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
  • lines changed 55, context: html, text, full: html, text
    060985eeea466cb4321e1e5e8c6401b62290f3ca Wed May 1 13:15:03 2019 -0700
    correctly finding table for list chromosome function with database table refs #18869
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    b1a610b0bcf08c2ed4688253801d8039b64380f2 Wed May 1 14:17:16 2019 -0700
    only allow positon tables on list chromosomes when table requested refs #18869
  • lines changed 27, context: html, text, full: html, text
    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/err15.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err21.gz
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    84b4398cfba70b1faf3ecff87404f0884aef4be6 Thu May 2 10:27:48 2019 -0700
    correcting err21 test refs #18869
• src/hg/hubApi/tests/expected/err24.gz
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    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
• src/hg/hubApi/tests/expected/err30.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err31.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err32.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err33.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err34.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/expected/err35.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
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    1b5d4cf1c155cb8afbbf5f635e16c8b396be5de6 Thu May 2 14:31:02 2019 -0700
    fixing err35 and err36 outputs refs #18869
• src/hg/hubApi/tests/expected/err36.gz
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
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    1b5d4cf1c155cb8afbbf5f635e16c8b396be5de6 Thu May 2 14:31:02 2019 -0700
    fixing err35 and err36 outputs refs #18869
• src/hg/hubApi/tests/expected/err37.gz
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    6d310e4d8a6999ac3d20a1d44b114ae7591bfef6 Thu May 2 15:06:14 2019 -0700
    add tests for illegal values to arguments and duplicated argument refs #18869
• src/hg/hubApi/tests/expected/err38.gz
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    6d310e4d8a6999ac3d20a1d44b114ae7591bfef6 Thu May 2 15:06:14 2019 -0700
    add tests for illegal values to arguments and duplicated argument refs #18869
• src/hg/hubApi/tests/expected/list01.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list02.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list03.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list04.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list05.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list06.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list07.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list08.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list09.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list10.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list11.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list12.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list13.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list14.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/list15.gz
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
• src/hg/hubApi/tests/expected/notSup01.gz
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    b59e6fc00f9ce106f08d9bada4b9e95b67843aa3 Tue Apr 30 10:58:59 2019 -0700
    testing non supported track types refs #18869
• src/hg/hubApi/tests/expected/notSup02.gz
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    b59e6fc00f9ce106f08d9bada4b9e95b67843aa3 Tue Apr 30 10:58:59 2019 -0700
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    811d634fc8b02a1f9156a002262a2763544682e5 Thu May 2 10:11:46 2019 -0700
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• src/hg/hubApi/tests/expected/test17.gz
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    aafa5935720a50d8e9c9c1ce88c2e7e93c4642ab Tue Apr 30 10:16:36 2019 -0700
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• src/hg/hubApi/tests/expected/test18.gz
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• src/hg/hubApi/tests/expected/test2.gz
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• src/hg/hubApi/tests/expected/test22.gz
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• src/hg/hubApi/tests/expected/test23.gz
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• src/hg/hubApi/tests/expected/test3.gz
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• src/hg/hubApi/tests/expected/test30.gz
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    811d634fc8b02a1f9156a002262a2763544682e5 Thu May 2 10:11:46 2019 -0700
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• src/hg/hubApi/tests/expected/test31.gz
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    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
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    811d634fc8b02a1f9156a002262a2763544682e5 Thu May 2 10:11:46 2019 -0700
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• src/hg/hubApi/tests/expected/test41.gz
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    aafa5935720a50d8e9c9c1ce88c2e7e93c4642ab Tue Apr 30 10:16:36 2019 -0700
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• src/hg/hubApi/tests/expected/test42.gz
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    aafa5935720a50d8e9c9c1ce88c2e7e93c4642ab Tue Apr 30 10:16:36 2019 -0700
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• src/hg/hubApi/tests/expected/test5.gz
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    811d634fc8b02a1f9156a002262a2763544682e5 Thu May 2 10:11:46 2019 -0700
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• src/hg/hubApi/tests/expected/wig01.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
• src/hg/hubApi/tests/expected/wig02.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig03.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig04.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig05.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig06.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig07.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig08.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig09.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig10.gz
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• src/hg/hubApi/tests/expected/wig11.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig12.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig13.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig14.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig15.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
• src/hg/hubApi/tests/expected/wig16.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig17.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
• src/hg/hubApi/tests/expected/wig18.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig19.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig20.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig21.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig22.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig23.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
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• src/hg/hubApi/tests/expected/wig24.gz
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
• src/hg/hubApi/tests/jsonConsumer.pl
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
• src/hg/hubApi/tests/makefile
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    527d5b5e1e77777e67a1f69d19e615e850258570 Tue Apr 30 09:46:00 2019 -0700
    fixup wiggle output itemCount refs #18869
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    3df39731a0de10c2a708ce19d3022bb66b890085 Tue Apr 30 10:19:01 2019 -0700
    moved test41 test42 to other category refs #18869
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    b59e6fc00f9ce106f08d9bada4b9e95b67843aa3 Tue Apr 30 10:58:59 2019 -0700
    testing non supported track types refs #18869
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    e28cc42abe8dbb30decf688ad7be6d593fcc8b75 Tue Apr 30 15:56:20 2019 -0700
    adding extraneous argument checks for all functions to cause error refs #18869
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    2d0e3b500f8e1d5f1ecf372797f942204fa729b8 Thu May 2 10:08:25 2019 -0700
    correctly manage list chromosomes function with various table types refs #18869
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    84b4398cfba70b1faf3ecff87404f0884aef4be6 Thu May 2 10:27:48 2019 -0700
    correcting err21 test refs #18869
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    722e3f4e77c812ebb31bb1533a4918f0cab8fee4 Thu May 2 11:37:03 2019 -0700
    adding tests to check for extraneous arguments refs #18869
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    1b5d4cf1c155cb8afbbf5f635e16c8b396be5de6 Thu May 2 14:31:02 2019 -0700
    fixing err35 and err36 outputs refs #18869
• src/hg/inc/soTerm.h
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    9a5c1dc41298119f9569b12985a34146212dfe1a Wed Apr 10 09:36:38 2019 -0700
    Added soTermStringIdToId, soTermCmp, and soTermToMisoLink, for use with new dbSNP data. refs #23283
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    0c882cb50cc196e069a5df0f19cb83997d6d3882 Tue Apr 16 14:00:17 2019 -0700
    Added SO terms used in dbSNP b152 JSON, plus an soUnknown enum value for when no SO terms are assigned. Move up nc_transcript_variant in funcImpactOrder to be above up/downstream. refs #23283
• src/hg/inc/trackHub.h
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    d0df5dc6ead611a45dda4ccbd0da5e5917ad3532 Wed May 1 16:18:42 2019 -0700
    Reverting the missing children check after lots of discussion, refs #23418
• src/hg/js/hgTracks.js
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    93f9a02e8a70606f70c425971bb1d961eec3d080 Tue Apr 30 00:53:00 2019 -0700
    first try to fix too-small highlight bug, refs #23349
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    1fcd74f4187843438947883d02d248108f918840 Tue Apr 30 13:55:32 2019 -0700
    Revert "first try to fix too-small highlight bug, refs #23349" This reverts commit 93f9a02e8a70606f70c425971bb1d961eec3d080.
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    8be71ea001dc92c31702850b82736793299214eb Tue Apr 30 13:58:44 2019 -0700
    fix for between-bp highlight bug, many thanks to Angie for fixing my fix, refs #23349 and related build patch
• src/hg/lib/gdcCancer.as
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    4e6eb7db020f87bdc9f63f347cee9a080251f0fa Wed May 1 15:00:06 2019 -0700
    clean up GDC Cancer AS file
• src/hg/lib/hui.c
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    673f0be0f4a353fe2f64bad5623da55b9c2ee9eb Wed May 1 15:17:00 2019 -0700
    add yet another bigLolly to an if statement
• src/hg/lib/soTerm.c
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    9a5c1dc41298119f9569b12985a34146212dfe1a Wed Apr 10 09:36:38 2019 -0700
    Added soTermStringIdToId, soTermCmp, and soTermToMisoLink, for use with new dbSNP data. refs #23283
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    0c882cb50cc196e069a5df0f19cb83997d6d3882 Tue Apr 16 14:00:17 2019 -0700
    Added SO terms used in dbSNP b152 JSON, plus an soUnknown enum value for when no SO terms are assigned. Move up nc_transcript_variant in funcImpactOrder to be above up/downstream. refs #23283
• src/hg/lib/trackHub.c
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    c66047d34f4a5e0df8f273a98531de3b942556eb Wed May 1 12:53:12 2019 -0700
    Fixing bug in checking for subtracks of superTracks, composites and views as pointed out by Jonathan, refs #22397
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    d0df5dc6ead611a45dda4ccbd0da5e5917ad3532 Wed May 1 16:18:42 2019 -0700
    Reverting the missing children check after lots of discussion, refs #23418
• src/hg/makeDb/doc/hg38/gdcCancer.txt
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    4e6eb7db020f87bdc9f63f347cee9a080251f0fa Wed May 1 15:00:06 2019 -0700
    clean up GDC Cancer AS file
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    e2d3d27d2095535a171f5e8e7aa965633189138a Fri May 3 15:54:15 2019 -0700
    add separate tracks for each project in the GDC Cancer composite
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
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    09f8c57bea92e646e7cc4ac1d20a09d585ffe5e5 Fri May 3 08:33:57 2019 -0700
    Updating http to https for galGal6, uiLinks cronjob.
• src/hg/makeDb/trackDb/crispr10K.html
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    09f8c57bea92e646e7cc4ac1d20a09d585ffe5e5 Fri May 3 08:33:57 2019 -0700
    Updating http to https for galGal6, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124way.ra
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    aa5de6adb2f48a0eb96f78d6c0e84199c692369e Wed May 1 09:08:29 2019 -0700
    Removing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/fugu/fr2/gap.html
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    a2c6bef0f60ab7df64cc0b61589ba5d52568b5a4 Thu May 2 09:53:17 2019 -0700
    Upating http to https for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
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    a2c6bef0f60ab7df64cc0b61589ba5d52568b5a4 Thu May 2 09:53:17 2019 -0700
    Upating http to https for fr2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
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    e2d3d27d2095535a171f5e8e7aa965633189138a Fri May 3 15:54:15 2019 -0700
    add separate tracks for each project in the GDC Cancer composite
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
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    aa5de6adb2f48a0eb96f78d6c0e84199c692369e Wed May 1 09:08:29 2019 -0700
    Removing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
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    ff5d05e56e760c6cc49797158e66d074088d9b86 Fri May 3 09:45:54 2019 -0700
    Changing All GENCODE track name for mm10 now that default genes track is also GENCODE #23284
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    38aed9a87ffb6dfe6550f81318e4989c209ec0d1 Tue Apr 30 09:29:58 2019 -0700
    Updating http to https for mm7, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/phastConsElements17way.html
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    38aed9a87ffb6dfe6550f81318e4989c209ec0d1 Tue Apr 30 09:29:58 2019 -0700
    Updating http to https for mm7, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
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    38aed9a87ffb6dfe6550f81318e4989c209ec0d1 Tue Apr 30 09:29:58 2019 -0700
    Updating http to https for mm7, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/rikenCageTc.html
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    38aed9a87ffb6dfe6550f81318e4989c209ec0d1 Tue Apr 30 09:29:58 2019 -0700
    Updating http to https for mm7, uiLinks cronjob.
• src/hg/utils/binFromRange/binFromRange.c
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    9f568df48c409c062eab6e3b2aa60bc8509bf120 Fri May 3 16:42:33 2019 -0700
    binFromRange: util to convert start and end coords into a SQL '(bin = ### or bin = ### ...)' condition. refs #23429
• src/hg/utils/binFromRange/makefile
  • lines changed 3, context: html, text, full: html, text
    9f568df48c409c062eab6e3b2aa60bc8509bf120 Fri May 3 16:42:33 2019 -0700
    binFromRange: util to convert start and end coords into a SQL '(bin = ### or bin = ### ...)' condition. refs #23429
• src/hg/utils/hubCheck/hubCheck.c
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    d0df5dc6ead611a45dda4ccbd0da5e5917ad3532 Wed May 1 16:18:42 2019 -0700
    Reverting the missing children check after lots of discussion, refs #23418
• src/hg/utils/jsonQuery/jsonQuery.c
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    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/hg/utils/jsonQuery/makefile
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    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/hg/utils/makefile
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    9f568df48c409c062eab6e3b2aa60bc8509bf120 Fri May 3 16:42:33 2019 -0700
    binFromRange: util to convert start and end coords into a SQL '(bin = ### or bin = ### ...)' condition. refs #23429
• src/inc/common.h
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    4d1e38588ee18350611bbe576a7ceb91d5812e65 Tue Apr 16 14:01:29 2019 -0700
    Added const to declarations of some char * function params that are not modified, so I can use const in calling routines.
• src/inc/hash.h
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    bc5a73ec376d9d06861b8d07e7abfe615fc38501 Wed Apr 10 09:39:10 2019 -0700
    Added hashIntReset, to quickly remove & reset to 0 all integer values of a hash. [It can also NULL out hashEl pointers, but mem alloc issues should be considered]
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    506484c03bae4b9a7d61c5a56b928e773a0c83a7 Tue Apr 16 14:02:22 2019 -0700
    Added hashNewLm/newHashLm so an external lm can be passed in and used for all hash allocations.
• src/inc/jsonParse.h
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    92ff3a19fc5cacf7b92a1a25086d9300f7df53e0 Tue Apr 16 14:02:52 2019 -0700
    Added *Lm functions that optionally use lm to allocate memory. Removed unused jsonFindName* functions -- if needed in the future, jsonQuery will probably be easier to use.
• src/inc/jsonQuery.h
  • lines changed 57, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/inc/localmem.h
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    4d1e38588ee18350611bbe576a7ceb91d5812e65 Tue Apr 16 14:01:29 2019 -0700
    Added const to declarations of some char * function params that are not modified, so I can use const in calling routines.
• src/lib/basicBed.c
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    9d47270703d4b9b603127f6c41dc9f1e49b56708 Wed Apr 17 11:08:58 2019 -0700
    loadAndValidateBed: Don't errAbort on empty array when checking autoSql fields; empty arrays are valid.
• src/lib/common.c
  • lines changed 4, context: html, text, full: html, text
    4d1e38588ee18350611bbe576a7ceb91d5812e65 Tue Apr 16 14:01:29 2019 -0700
    Added const to declarations of some char * function params that are not modified, so I can use const in calling routines.
• src/lib/hash.c
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    bc5a73ec376d9d06861b8d07e7abfe615fc38501 Wed Apr 10 09:39:10 2019 -0700
    Added hashIntReset, to quickly remove & reset to 0 all integer values of a hash. [It can also NULL out hashEl pointers, but mem alloc issues should be considered]
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    506484c03bae4b9a7d61c5a56b928e773a0c83a7 Tue Apr 16 14:02:22 2019 -0700
    Added hashNewLm/newHashLm so an external lm can be passed in and used for all hash allocations.
• src/lib/jsonParse.c
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    92ff3a19fc5cacf7b92a1a25086d9300f7df53e0 Tue Apr 16 14:02:52 2019 -0700
    Added *Lm functions that optionally use lm to allocate memory. Removed unused jsonFindName* functions -- if needed in the future, jsonQuery will probably be easier to use.
• src/lib/jsonQuery.c
  • lines changed 407, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/localmem.c
  • lines changed 5, context: html, text, full: html, text
    4d1e38588ee18350611bbe576a7ceb91d5812e65 Tue Apr 16 14:01:29 2019 -0700
    Added const to declarations of some char * function params that are not modified, so I can use const in calling routines.
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    7c84fe77d95b0733fcd4b27d8cbdfc038c1a8d5c Wed May 1 09:47:25 2019 -0700
    lmCleanup: null out *pLm before freeing lm, to make valgrind --leak-check=full -v happy.
• src/lib/makefile
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    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/tests/expected/jsonQueryTest.out
  • lines changed 190, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/tests/input/jsonQueryTestJson.txt
  • lines changed 5, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/tests/input/jsonQueryTestPath.txt
  • lines changed 18, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/tests/jsonQueryTest.c
  • lines changed 169, context: html, text, full: html, text
    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/lib/tests/makefile
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    b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700
    Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
• src/product/installer/browserSetup.sh
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    23b7a45a300da47bf35cf10780985699c1c9ac1b Tue Apr 30 01:51:48 2019 -0700
    todo for gbic
• src/utils/qa/weeklybld/buildEnv.csh
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    af07465d52b25936c5c185d8fbe68b0e8c7a5bfd Mon May 6 09:58:34 2019 -0700
    v382 preview1, refs #23326
• src/utils/qa/weeklybld/sendLogEmail.pl
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    c92592e733745a06c02be1b7ceba1e857b2daeeb Tue Apr 30 09:53:29 2019 -0700
    Resetting the Code Summaries to send to BrianL instead of AnnZ in sendLogEmail.pl

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• files changed: 195