All File Changes

v376_preview to v376_preview2 (2018-12-17 to 2019-01-07) v376

• README
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    9fa6ac13d910ceca97bfc81224325e23ee44b9c8 Tue Dec 18 10:56:50 2018 +0100
    adding version info to top level README, refs #22591
• confs/rr.hg.conf
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    21a8f84e97c68f39007abebc7ccab6c70743cddd Sun Dec 23 01:11:32 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGeneData/C_elegans/links.ra
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    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/Human/links.ra
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    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/Mouse/links.ra
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    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/Rat/links.ra
  • lines changed 1, context: html, text, full: html, text
    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
  • lines changed 6, context: html, text, full: html, text
    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/S_cerevisiae/links.ra
  • lines changed 1, context: html, text, full: html, text
    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 12, context: html, text, full: html, text
    4e4dfbf25a62cf80bc7ea9db0414dc1e10af894f Wed Dec 19 09:17:31 2018 -0800
    Removing broken links from links.ra files in hgGene , refs #15342
• src/hg/hgSession/hgSession.c
  • lines changed 27, context: html, text, full: html, text
    6ba4e724f84f86544c11a90f3802fd6318cd154f Fri Dec 21 16:28:42 2018 -0800
    Watch out for invalid data and unencoded newlines when reading in file uploaded as a saved session. refs #22638, #22637 cartLoadSettings did absolutely no checking that its input looked anything like cart settings, resulting in giant useless carts in which custom track files, hgTracks HTML and other arbitrary files apparently were parsed as cart settings. Now we do quite a bit of checking in cartLoadSettingsFromUserInput, and can warn the user if it looks like they are attempting to upload a custom track as a saved session. The unencoded newlines are our fault -- since 2010, we have been writing out saved session files without encoding newlines in setting values (pasted in by the user). Then those newlines can be mistaken for the newlines that we use to separate settings. Oops! Use a heuristic that holds up so far to determine whether the newlines should have been encoded: they seem to occur in specific variables (like hgta_pastedIdentifiers), and those variables always appear in the middle of an alphabetically sorted cluster of variables with the same prefix (like hgta_). And of course, we now write out saved session files with encoded newlines, which we decode when reading back in. We even have to deal with carts that have mixed types of newlines from various garbage sources, using lineFileCarefulNewlines().
  • lines changed 8, context: html, text, full: html, text
    1c72b82e508437dbb1bda1e9b812ea9f10090a30 Wed Dec 26 11:22:22 2018 -0800
    session thumbnail creation was failing with the short link option, so add a flag to return regular links, refs #8520
• src/hg/hgTables/bigBed.c
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    06c0276e636ee477a2a62187e066a89b230bb540 Mon Dec 17 15:51:35 2018 -0800
    Table schema shows update time for bigBed file instead of table, refs #22619
• src/hg/hgTracks/wigMafTrack.c
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    081e0431f88cf0536f1c4c56e56c3a0007890ab0 Wed Jan 2 13:20:26 2019 -0800
    speed up display for codonDefault AA display refs #19937
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    c8da620b1e51e27548201a8f4aa16bbc4d9aaecc Mon Jan 7 10:13:30 2019 -0800
    add to comment about speed up display refs #19937
• src/hg/htdocs/FAQ/FAQdownloads.html
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    5d4e325ceddb7e4a06bbe2be78476c9a21ed1332 Thu Jan 3 11:38:42 2019 -0800
    adding notes about command-line utilitiy executablilty to docs, refs #22684
• src/hg/htdocs/FAQ/FAQformat.html
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    4f2aded823c32161fbbe7e69ef955e3efb68cbbf Tue Dec 18 09:17:06 2018 -0800
    Adding hyphen in ASCII-combatible
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 87, context: html, text, full: html, text
    531970b3263a93145809039995210fa4edbeee63 Fri Dec 21 13:07:40 2018 +0100
    adding stub for genes faq page, refs #22696 #21987
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 3, context: html, text, full: html, text
    725983f4b5be461a26b255a479cb93bfe9741e83 Wed Dec 19 10:28:13 2018 -0800
    Adding notes about bigWigToWig utility returning bedGraph for bedGraph originating bigWigs
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 16, context: html, text, full: html, text
    35db919bb28315aa5911457e504e3195fb258901 Thu Dec 20 10:11:51 2018 -0800
    Emphasizing (type bidBed # +) in Track hub docs to access extra fields, refs #21572
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    b6dfe315c5478f41de9b785e798f448f3664ec45 Wed Jan 2 16:27:09 2019 -0800
    editing bigBed.html to explain -type=bedN[+[P]], refs #21572
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 3, context: html, text, full: html, text
    725983f4b5be461a26b255a479cb93bfe9741e83 Wed Dec 19 10:28:13 2018 -0800
    Adding notes about bigWigToWig utility returning bedGraph for bedGraph originating bigWigs
• src/hg/htdocs/goldenPath/help/chimera.html
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    4843722b8748e5745d92ece1c2bfcc30b8d495ea Wed Dec 19 16:21:16 2018 -0800
    Fixing broken 404 link ref#9677
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 25, context: html, text, full: html, text
    c36babd397ab3352e39ddbde424076fcf9b121a4 Tue Dec 18 11:38:26 2018 +0100
    adding docs about big* files hosting, refs #20224
  • lines changed 15, context: html, text, full: html, text
    30aeefa0d5dd7977c84a5c56a55ead65b449bc78 Wed Dec 19 16:51:20 2018 -0800
    Fixing broken link and adding info about dropbox no longer allowing public data links.
  • lines changed 7, context: html, text, full: html, text
    40d30fdd5f3e864a47fbf8d791e0b599a6593e4b Thu Dec 20 10:42:55 2018 -0800
    Add example using rsid directly in the URL ref#22331
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    2f7b5f9d36a0bc8db58af038e8beef47d95a9aa5 Thu Dec 20 12:08:02 2018 -0800
    Removed extra period
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    9ae00e4669a53c7b26de2ad96ba82e2e1f663618 Thu Dec 20 16:29:18 2018 -0800
    Replaced improperly ordered example titles
  • lines changed 147, context: html, text, full: html, text
    5043350a1f0737ef2224ce5d28b9012711ce0b01 Thu Dec 20 17:31:10 2018 -0800
    Added <dd> and <dt> tags to reduce padding according to html template #22335
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    8b3912779b2282020a9c41375ea5ce28455f597f Thu Dec 20 17:53:09 2018 -0800
    Removed improper use of <dd> and <dt> tags.#22335
  • lines changed 2, context: html, text, full: html, text
    93e7073e9fa1f0778ec5e2719abc2a849270aebf Fri Dec 21 10:08:12 2018 -0800
    HTML formatting, minor example updates #22335
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    337b3185e1f1966cc28c279da04026ef6d226c87 Fri Dec 21 10:29:25 2018 -0800
    HTML formatting updates #22335
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    d49f2f9f6c1fae573dc7e6744de4540f2c2c2ea6 Fri Dec 21 11:22:32 2018 -0800
    Fixing merge conflict
  • lines changed 137, context: html, text, full: html, text
    f0fe71c7a1167f8d3ea77261ea47d1566e091cb2 Fri Dec 21 11:45:13 2018 -0800
    Took out errant <dd> and <dt> tags
  • lines changed 4, context: html, text, full: html, text
    2b00aa93e08e3cc7113bd778f52882c6079b0e7b Fri Jan 4 13:23:40 2019 -0800
    adding documentation to customTrack.html about type bigBed+, refs #21572
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    c92dabf2ba25a826e9cc6aa5487a371e26b7dc2b Fri Jan 4 15:45:22 2019 -0800
    Adding 'type bigBed # +' to customTrack.html and trackDbHub.html documentation, refs #21572
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    fd35a0978829305c6423aa3be50b2a043845b5db Mon Jan 7 09:12:22 2019 -0800
    Adding 'type bigBed # +' to customTrack.html and TrackDb Library.shtml, refs #21572
• src/hg/htdocs/goldenPath/help/gbib.html
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    8b067e54d43ccbaf69547d3559cec89763878e78 Mon Dec 17 13:32:47 2018 -0800
    Adding a new line character to reduce amount of characters in one line
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    c36babd397ab3352e39ddbde424076fcf9b121a4 Tue Dec 18 11:38:26 2018 +0100
    adding docs about big* files hosting, refs #20224
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    77d6420dda837c8a6ce888b359bff00a07351f17 Wed Dec 19 17:09:08 2018 -0800
    Adding note about cloud storage providers not working as data hosts
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    36f6c19a57e047b776b8b8c8b71b0d7b88b8aaaf Fri Dec 21 13:09:03 2018 +0100
    extending track hub help
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
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    983d076eec1573b48a6a8204796deb2019702555 Thu Dec 20 13:35:54 2018 -0800
    fixing broken 404 links on static doc pages, refs #9677
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
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    35db919bb28315aa5911457e504e3195fb258901 Thu Dec 20 10:11:51 2018 -0800
    Emphasizing (type bidBed # +) in Track hub docs to access extra fields, refs #21572
• src/hg/htdocs/goldenPath/help/mirror.html
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    77b5a7411e5454163763d70e9bc5a69f6cdc1d14 Fri Dec 14 11:55:43 2018 -0800
    Removing dead links on mirror.html page ref#22339
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    29099f7d8866e0a55b2b8d9539e7ee3d47cb14f3 Fri Dec 14 13:26:13 2018 -0800
    Fixing a sentence missing a word in mirror.html, no RM
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    983d076eec1573b48a6a8204796deb2019702555 Thu Dec 20 13:35:54 2018 -0800
    fixing broken 404 links on static doc pages, refs #9677
• src/hg/htdocs/goldenPath/help/oligoMatch.html
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    983d076eec1573b48a6a8204796deb2019702555 Thu Dec 20 13:35:54 2018 -0800
    fixing broken 404 links on static doc pages, refs #9677
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
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    dcd0eb48636d64046e082de504e9983372078d0f Mon Jan 7 09:26:54 2019 -0800
    Removing additional directUrl line mistakenly added by me to try to trigger Table Of Contents link, refs #22711 #22714
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    c92dabf2ba25a826e9cc6aa5487a371e26b7dc2b Fri Jan 4 15:45:22 2019 -0800
    Adding 'type bigBed # +' to customTrack.html and trackDbHub.html documentation, refs #21572
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    fd35a0978829305c6423aa3be50b2a043845b5db Mon Jan 7 09:12:22 2019 -0800
    Adding 'type bigBed # +' to customTrack.html and TrackDb Library.shtml, refs #21572
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    8babfe023086d32d15969da38698683525d15975 Mon Jan 7 09:46:47 2019 -0800
    Correcting example to have space before + in type bigBed 9 +
• src/hg/htdocs/goldenPath/help/wiggle.html
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    725983f4b5be461a26b255a479cb93bfe9741e83 Wed Dec 19 10:28:13 2018 -0800
    Adding notes about bigWigToWig utility returning bedGraph for bedGraph originating bigWigs
• src/hg/htdocs/gtex.html
  • lines changed 84, context: html, text, full: html, text
    2ab662767ea06905eb431182ac306c37f9a606e8 Mon Dec 17 18:51:32 2018 -0800
    Initial draft of GTEx static page. refs #22678
  • lines changed 9, context: html, text, full: html, text
    3168dd0559705837dccfb2e783b8d5e4212356a2 Mon Dec 17 19:10:34 2018 -0800
    Add description line for each track and hub. refs #22678
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    464cf388b1a0b858741f8d5e3b851813cec724a0 Mon Dec 17 19:11:59 2018 -0800
    Restore image credit. refs #22678
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    e37b391a14c26fd75b24710af0d70277fdd53aba Wed Dec 19 10:53:36 2018 -0800
    Improve images. refs #22678
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    c237ff6e1ad9fafe1b5a55e3abb85e590567aaed Wed Dec 19 17:37:41 2018 -0800
    Cosmetic layout changes. refs #22678
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    6a29084f212692a91c4f7a86ac2e8d7265f3a05e Wed Dec 19 17:42:59 2018 -0800
    Tweak description. refs #22678
• src/hg/htdocs/images/Eulemur_flavifrons,jpg
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    2f39747123c131d22d82f2bc661fb6a82f3a658e Thu Jan 3 13:13:07 2019 -0800
    remove bogus file name with comma in place of period no redmine
• src/hg/htdocs/images/gtexBlogSession.png
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    2ab662767ea06905eb431182ac306c37f9a606e8 Mon Dec 17 18:51:32 2018 -0800
    Initial draft of GTEx static page. refs #22678
• src/hg/htdocs/images/gtexSessionGeneExpr.png
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    d4729c810e5ebea724b313842b494f717ab2800f Wed Dec 19 17:41:43 2018 -0800
    Improved image for example session. refs #22678
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
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    6c1eb688828f6d49875b85ac74e151460ac87334 Wed Dec 26 08:22:08 2018 -0800
    Encoding an ampersand in HTML, no Redmine.
• src/hg/inc/cart.h
  • lines changed 20, context: html, text, full: html, text
    6ba4e724f84f86544c11a90f3802fd6318cd154f Fri Dec 21 16:28:42 2018 -0800
    Watch out for invalid data and unencoded newlines when reading in file uploaded as a saved session. refs #22638, #22637 cartLoadSettings did absolutely no checking that its input looked anything like cart settings, resulting in giant useless carts in which custom track files, hgTracks HTML and other arbitrary files apparently were parsed as cart settings. Now we do quite a bit of checking in cartLoadSettingsFromUserInput, and can warn the user if it looks like they are attempting to upload a custom track as a saved session. The unencoded newlines are our fault -- since 2010, we have been writing out saved session files without encoding newlines in setting values (pasted in by the user). Then those newlines can be mistaken for the newlines that we use to separate settings. Oops! Use a heuristic that holds up so far to determine whether the newlines should have been encoded: they seem to occur in specific variables (like hgta_pastedIdentifiers), and those variables always appear in the middle of an alphabetically sorted cluster of variables with the same prefix (like hgta_). And of course, we now write out saved session files with encoded newlines, which we decode when reading back in. We even have to deal with carts that have mixed types of newlines from various garbage sources, using lineFileCarefulNewlines().
• src/hg/lib/botDelay.c
  • lines changed 13, context: html, text, full: html, text
    7f57dde74b07fca259053625e2532935d7f617e0 Fri Jan 4 02:47:24 2019 -0800
    adding URL to botDelay message, refs #22716
• src/hg/lib/cart.c
  • lines changed 581, context: html, text, full: html, text
    6ba4e724f84f86544c11a90f3802fd6318cd154f Fri Dec 21 16:28:42 2018 -0800
    Watch out for invalid data and unencoded newlines when reading in file uploaded as a saved session. refs #22638, #22637 cartLoadSettings did absolutely no checking that its input looked anything like cart settings, resulting in giant useless carts in which custom track files, hgTracks HTML and other arbitrary files apparently were parsed as cart settings. Now we do quite a bit of checking in cartLoadSettingsFromUserInput, and can warn the user if it looks like they are attempting to upload a custom track as a saved session. The unencoded newlines are our fault -- since 2010, we have been writing out saved session files without encoding newlines in setting values (pasted in by the user). Then those newlines can be mistaken for the newlines that we use to separate settings. Oops! Use a heuristic that holds up so far to determine whether the newlines should have been encoded: they seem to occur in specific variables (like hgta_pastedIdentifiers), and those variables always appear in the middle of an alphabetically sorted cluster of variables with the same prefix (like hgta_). And of course, we now write out saved session files with encoded newlines, which we decode when reading back in. We even have to deal with carts that have mixed types of newlines from various garbage sources, using lineFileCarefulNewlines().
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/ensFace.c
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    576ed6d352781ef9ea35cbde762907bba315c68e Thu Jan 3 06:06:57 2019 -0800
    fixing outlink to Ensembl, refs #22701
• src/hg/lib/jksql.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/knownCanonical.sql
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    c0a6048e07b4cae079738ca5b3cb076493dbd19e Fri Jan 4 10:00:37 2019 -0800
    modify some knownGene SQL files to use full query for index #22713
• src/hg/lib/knownTo.sql
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    c0a6048e07b4cae079738ca5b3cb076493dbd19e Fri Jan 4 10:00:37 2019 -0800
    modify some knownGene SQL files to use full query for index #22713
• src/hg/lib/lav.c
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    9cc44f3539c422b2ccca8345eb0751439450dee0 Thu Dec 20 13:52:51 2018 -0800
    Fixing mem-overwriting bug found when linefile.c has an artificially low starting buffer size for testing. Doesn't apply in normal use, just fixing so I can test lineFile's buffering logic.
• src/hg/lib/pslReader.c
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    9466f0e71913fd917ee6c919a8a8b31edd59a9c0 Thu Jan 3 16:34:29 2019 -0800
    use all of query for index #22713
• src/hg/lib/snpTmp.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/lib/wigDataStream.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/makeDb/doc/bosTau6.txt
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    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau7.txt
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    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 14, context: html, text, full: html, text
    43c2ea2c14ffb39612182c7f98170f604ddf22ca Fri Dec 21 15:33:40 2018 -0800
    liftOvers to bosTau9 per user request refs #22399
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
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    f566f5f02dc7339e212d88659d811aed488c5fc8 Fri Dec 21 15:34:51 2018 -0800
    bosTau9 browser build done refs #22425
• src/hg/makeDb/doc/ce11/multiz135way.txt
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    1b14bc9f8f21671b91d698b48fcee080d668a2e1 Fri Dec 21 15:27:54 2018 -0800
    track complete QA Ready refs #22599
• src/hg/makeDb/doc/dm6/multiz124way.txt
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    b9e2880b0c244b4118ea0c1b445119cf7016e3a6 Wed Dec 19 16:03:01 2018 -0800
    restart multiz with new phylo tree refs @22550
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    1257fd0a18976f8dce7ba049cd5494285504fcfc Fri Dec 21 15:25:29 2018 -0800
    rework this track with a better phylo tree refs #22550
• src/hg/makeDb/doc/galGal6/initialBuild.txt
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    cf8e0c3e1c2ae902fe4acc06cfbfb08a0627a5d2 Fri Dec 21 15:37:41 2018 -0800
    finished cotJap2 lastz/chainNet and browser build complete refs #22113
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
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    cf8e0c3e1c2ae902fe4acc06cfbfb08a0627a5d2 Fri Dec 21 15:37:41 2018 -0800
    finished cotJap2 lastz/chainNet and browser build complete refs #22113
• src/hg/makeDb/doc/galGal6/multiz77way.txt
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    d3982d16735c2ac591fe480ae3775f417be29d6c Fri Dec 21 15:26:52 2018 -0800
    done with this track marked QA Ready refs #22687
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    5f17b51be966889b483a5a5495137683c752a08a Wed Jan 2 12:55:20 2019 -0800
    Update GeneHancer track with 4 corrected files provided by Simon F. #22712
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    2d27a24738cb880e57505cd71605072629c05368 Fri Dec 21 15:31:24 2018 -0800
    panTro6 and ponAbe3 liftOvers per user request refs #2657
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    f82654e4d16d4911e236d3e8faad58bd1b9b765b Fri Dec 21 15:38:38 2018 -0800
    completed 10K track refs #21575
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    b4098c773b944482ec48818e63b1518a90660d35 Fri Jan 4 11:07:36 2019 -0800
    use NCBI RefSeq instead of UCSC RefSeq for the CDS FASTA files
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    acdf58105d537fdcadff7a5f1dbaceebe1869dfe Fri Dec 21 15:42:21 2018 -0800
    liftOver to petMar3 for petMar3 browser release refs #20819
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    d90aaacb8b2c810a3689b8cd7f27ace9bd55d76b Fri Dec 21 15:57:17 2018 -0800
    running up crispr 10K to test fixes to the script refs #21987
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    c794f73d6f86f6d33fc75d10240eee1b6dcb1cbc Mon Dec 31 12:30:23 2018 -0800
    initial scripts to count mafGene AAs and construct AA profile composite track refs #19937
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    64636f495149ba1e1d52b785645d8fe4dbab3d00 Mon Dec 31 12:31:33 2018 -0800
    AA composite track now with mouse over data and color coding frequency refs #19937
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    9bf992fff5f52b6c8f915bb868f2d01d21cd7ce3 Thu Jan 3 15:50:24 2019 -0800
    script used to scan the gene definitions extracting descriptions for clicks on ncbiGene track refs #19937
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    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
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    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
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    c794f73d6f86f6d33fc75d10240eee1b6dcb1cbc Mon Dec 31 12:30:23 2018 -0800
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    64636f495149ba1e1d52b785645d8fe4dbab3d00 Mon Dec 31 12:31:33 2018 -0800
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    5eeb6064a4139903f43187b8c7d869752fdd9749 Sat Dec 29 12:32:26 2018 -0800
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• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh
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    3315cb5c5cb6380b15c17f7b9531dc4f33bdee49 Fri Jan 4 11:08:41 2019 -0800
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    e6e7df9527a71c876c262fdc42d16e1af0eef013 Wed Dec 26 07:19:27 2018 -0800
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    f698da27426bf0aa389780675b4238d0fb8f249b Wed Dec 26 11:51:06 2018 -0800
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    28690c391977a93ec08c0abda3fefb029a4b2d32 Wed Jan 2 16:21:35 2019 -0800
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• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    a6015a4f939b89fae9a99fb379d6ab5975be4f38 Wed Jan 2 16:24:53 2019 -0800
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    28690c391977a93ec08c0abda3fefb029a4b2d32 Wed Jan 2 16:21:35 2019 -0800
    adding staAur2 Staphylococcus aureus- refs #19937
• src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c
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    9744b1d0f27d7dcea4599b03e4b15a9e9970238a Thu Jan 3 13:09:50 2019 -0800
    blast tabs tables should index the entire query #2273
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    3a4ae2296f5def3c5d9d0fecf3c1971843249da3 Thu Jan 3 14:03:29 2019 -0800
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• src/hg/makeDb/trackDb/bacteria/staAur2/aaCounts.ra
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    a686a883905d058d863c2b7b277f009864a6820c Mon Dec 31 00:59:19 2018 -0800
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    f8a6772a141e5503918a6fea0d709b57f2d0944e Thu Jan 3 13:09:53 2019 -0800
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    68c17eba60f6a35a59ac8c836f8d42f6a9b176a1 Thu Dec 20 13:55:09 2018 -0800
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
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    37d56bf57d47b9942917c75ff7ce1de71c56ff55 Sun Dec 30 15:37:03 2018 -0800
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• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.369way.ra
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    e170cdd68db4a72147a96a8a7a8cc4fc6bed28cb Sat Dec 29 12:20:34 2018 -0800
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• src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra
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    02d6d5e6afdfca26ea2343fa551c7f247558cfa7 Thu Dec 20 13:55:15 2018 -0800
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    e170cdd68db4a72147a96a8a7a8cc4fc6bed28cb Sat Dec 29 12:20:34 2018 -0800
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    a686a883905d058d863c2b7b277f009864a6820c Mon Dec 31 00:59:19 2018 -0800
    adding composite track of AA profiles refs #19937
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    79a63f79023731177747e95e2fe8a75bbb152131 Mon Dec 31 18:38:24 2018 -0800
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    add the crispr 10K track refs #19937
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    63b37dcf81f1ed851ff43923826f00c94ee1c525 Thu Dec 20 09:11:06 2018 -0800
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    43446ffe54c2bc6edb87165e59a8f0fe1e5c4f58 Thu Dec 20 09:43:03 2018 -0800
    should be complete now refs #22687
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• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.77way.ra
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    14bffd2c4758a9164cc21109ca908ab9931eb197 Tue Dec 18 15:29:58 2018 -0800
    turning on frames refs #22687
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    5c6cc1f40eb88d7382260380f4a2e3dca8bc663c Mon Dec 31 05:27:20 2018 -0800
    fixing doc error on crispr page, pointed out by a ticket on the crispor github tracker, no redmine
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    5f17b51be966889b483a5a5495137683c752a08a Wed Jan 2 12:55:20 2019 -0800
    Update GeneHancer track with 4 corrected files provided by Simon F. #22712
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    d095048e8fb8d8cb5b4ba4223336ad136dc117be Wed Jan 2 09:30:33 2019 -0800
    Updating http to https and also fixing a link that was broken due to my script, uiLinks cronjob
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
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    Updating http to https and also fixing a link that was broken due to my script, uiLinks cronjob
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    0505afae76f4e9920c9282918ace35855714c866 Fri Dec 21 15:57:43 2018 -0800
    turn on crispr 10K track refs #21987
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    c6402974a2bd3d0b8c4c542bcefea44af208ceb4 Mon Dec 17 02:57:24 2018 -0800
    adding hgmd transcripts track, refs #22659
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    cac465e49829bf71bf49093f3e9e5cf95728e812 Wed Dec 19 22:07:11 2018 +0100
    removing release tag from ncbiRefSeqHgmd, even though we are supposed to add release tags when possible, apparently we cannot add release tags to subtracks of composites
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    9d4c61a944a3b928d0e5415f4ffd46f20b56a610 Thu Dec 20 08:15:42 2018 -0800
    adding refseq MANE, refs #22659
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    4e4157d5f7c461907adad8c2ce06ab89dadb6d6b Sat Dec 29 12:21:04 2018 -0800
    first peek at staAur2 369-way alignment refs #19937
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    6162d6e72a3d8f462747598076f900166ca3d21e Mon Dec 31 11:55:03 2018 -0800
    allow bedNameLabel on bigBed refs #19937
• src/hg/makeDb/trackDb/worm/caeRem2/ctgPos2.html
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    8a34ff74a6ad743d9f2c7991d47e2d12c4ebade6 Tue Dec 18 13:42:27 2018 -0800
    correct 112 nematodes 22 flatworms refs #22599
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    c86362180325cce597de07f851950546caff9d02 Wed Dec 19 08:18:27 2018 -0800
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    560967fb8867514d348760a6d70cadb641488e4a Thu Dec 20 09:57:04 2018 -0800
    correcting comments refs #22599
• src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra
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    8a34ff74a6ad743d9f2c7991d47e2d12c4ebade6 Tue Dec 18 13:42:27 2018 -0800
    correct 112 nematodes 22 flatworms refs #22599
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
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• src/hg/makeDb/trackDb/worm/chainCe4.html
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    3f97f523805e249626accd3c855ae2ed841b7d34 Thu Jan 3 15:29:44 2019 -0800
    use full query for index #22713
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    e0260964813a12bd5a33cbd662ae27f029369c3a Thu Jan 3 15:51:09 2019 -0800
    use all of query in index #22713
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    6096ae468c0bec9a0f6818d1a12136d9987ef3f1 Sun Jan 6 11:37:29 2019 -0800
    allocate some memory out of the heap instead of the stack, which was overflowing on huge sequences
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    6b6e1c15a73e157b9f811f11e7c7d2488e3cb435 Mon Jan 7 07:53:51 2019 -0800
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    a40a70471d623a9777faac53fbc39d1cbf11c35f Fri Dec 21 15:59:05 2018 -0800
    fix to tolerate non existent query database refs #19937
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
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    1969f496a39dcf1a66caec35800600f08dcff2f8 Fri Dec 21 16:03:33 2018 -0800
    more efficient construction of jobLists using the correct workhorse and now allow small cluster hub for some steps refs #21987
• src/hg/utils/automation/doGenscan.pl
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
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    a40a70471d623a9777faac53fbc39d1cbf11c35f Fri Dec 21 15:59:05 2018 -0800
    fix to tolerate non existent query database refs #19937
• src/hg/utils/automation/doRepeatMasker.pl
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    f36151f6f2352441aa81fecbc376a8bd78d20632 Fri Dec 21 16:01:36 2018 -0800
    new location for program on ku kluster no more /scratch/data/ available refs #19937
• src/hg/utils/automation/makeDownloads.pl
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    adbe1dc27ea368dd35f6b1158c3a4c583d1f0d4a Thu Jan 3 14:49:47 2019 -0800
    eliminate /scratch/data/ cluster dependencies no longer present no redmine
• src/hg/utils/automation/makePushQSql.pl
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    052576da94f31940e692de6e244968418fd31f06 Tue Dec 18 15:39:47 2018 -0800
    add the ncbiRefSeq files to the gbdb listings refs #22113
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/hg/utils/otto/omim/flagOmimGene.py
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    05b1ed9198d08ec49ee4ca5b7e13d3c60b6e0080 Thu Jan 3 15:20:26 2019 -0800
    Fixing program name typo after code review, refs #22665
• src/hg/utils/phyloTrees/220way.nh
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    1967851cf7755877a221ade09aac480a7939aa13 Fri Dec 21 16:15:20 2018 -0800
    updating cotJap1 to cotJap2 refs #22687
• src/hg/utils/phyloTrees/asciiTree.pl
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    20094a79ca19c05188a331fa277552ece2da0a87 Fri Dec 21 16:14:42 2018 -0800
    need to take out all right parens) not just the first one refs #22687
• src/hg/utils/phyloTrees/binaryTree.pl
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    e99476a29297b7c4b01d7d71b6c256b407cd215a Sun Dec 23 14:55:16 2018 -0800
    correctly print out distances in floating point no scientific notation from TreeGraph2 refs #19937
• src/hg/utils/phyloTrees/commonNames.sh
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    07509b76c3ce5203539c9813c9403b0620261f6b Fri Dec 21 16:13:55 2018 -0800
    adding some updated assembly names refs #22687
• src/hg/utils/phyloTrees/vertebrates.txt
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    e47cec19ac058f45cd8c5b102895392b4e3c3bd4 Fri Dec 21 16:16:07 2018 -0800
    adding ambMex for Axoloti refs #21715
• src/htslib/vcf.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/inc/common.mk
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    630afe3b1e9cfddb738dadfd77bcde6b74c15dbf Sat Jan 5 16:20:18 2019 -0800
    using some static libraries on ubuntu with gcc-7 no redmine
• src/inc/linefile.h
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    bbeeeeb5d888089a025aa547c05bfc9b443dc39f Thu Dec 20 14:06:39 2018 -0800
    Adding support for files that may have a mix of newline styles (\r\n, \r, \n), enabled by calling lineFileCarefulNewlines. refs #22638 Scanning for any type of newline is not quite as efficient as scanning for only one pre-determined type, but it's necessary to deal with the kind of garbage data that has snuck into some saved sessions. I also fixed a couple subtle cases that have not caused any trouble in our day-to-day dealings with nice \n-separated input with line sizes shorter than the default lf->buf size (64k): * determineNlType initialized lf->nlType to UNIX, but if the first non-empty buffer did not contain any newline, UNIX may or may not have been the correct type. * The second time determineNlType was called, it was using an outdated endIx. Note the second instance of scanning for newlines used < sizeLeft as a test instead of endIx; that needed to be applied to determineNlType too. * determineNlType was called with buf+endIx, but with a byte limit that didn't account for endIx. I tested lineFile with an initial buf size of 16 (in lineFileAttach) to test the looping on gotLf.
• src/lib/dyOut.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/lib/linefile.c
  • lines changed 136, context: html, text, full: html, text
    bbeeeeb5d888089a025aa547c05bfc9b443dc39f Thu Dec 20 14:06:39 2018 -0800
    Adding support for files that may have a mix of newline styles (\r\n, \r, \n), enabled by calling lineFileCarefulNewlines. refs #22638 Scanning for any type of newline is not quite as efficient as scanning for only one pre-determined type, but it's necessary to deal with the kind of garbage data that has snuck into some saved sessions. I also fixed a couple subtle cases that have not caused any trouble in our day-to-day dealings with nice \n-separated input with line sizes shorter than the default lf->buf size (64k): * determineNlType initialized lf->nlType to UNIX, but if the first non-empty buffer did not contain any newline, UNIX may or may not have been the correct type. * The second time determineNlType was called, it was using an outdated endIx. Note the second instance of scanning for newlines used < sizeLeft as a test instead of endIx; that needed to be applied to determineNlType too. * determineNlType was called with buf+endIx, but with a byte limit that didn't account for endIx. I tested lineFile with an initial buf size of 16 (in lineFileAttach) to test the looping on gotLf.
• src/lib/maf.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine
• src/lib/udc.c
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    9d07701582c965f0bdaa23a73fdfe6dbf88d9a43 Thu Dec 20 16:54:07 2018 -0800
    added notes on how open-ended requests allow reusing sockets
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    49699b90510448dc894740cb369ee2ecada8eeea Sun Dec 23 10:27:15 2018 -0800
    added more notes on why UDC works the way it doesn
• src/utils/qa/weeklybld/buildEnv.csh
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    c35eeaeb4e0f0ae5434278fc3a6badde03264163 Mon Jan 7 10:15:59 2019 -0800
    v376 preview2, refs #22686
• src/utils/twoBitDup/twoBitDup.c
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    3aa934c99d7ce21128bebdf2d3b9055922901ec4 Sat Jan 5 15:38:11 2019 -0800
    mostly minor cosmetic fixups to satisify gcc-7 warnings no redmine

• lines changed: 19374
• files changed: 190