All File Changes

v374_preview to v374_preview2 (2018-10-29 to 2018-11-05) v374

• python/lib/ucscGb/qa/tables/checkGapOverlap.py
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    00b6bc62ac74afaee5bcc2a63a428721ab080afc Wed Oct 31 17:06:24 2018 -0700
    Making some minor changes to qa scripts, refs #20980 #22364
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    2c9bffffec982bc04e38aa3f089c63967cf0c102 Fri Nov 2 13:14:47 2018 -0700
    Woops forgot one spot to allow zero length items, refs #22364
• src/hg/dbTrash/dbTrash.c
  • lines changed 20, context: html, text, full: html, text
    0d8013682ea0c2dcedf8c8639d78b8736be92ba4 Thu Nov 1 12:47:29 2018 -0700
    adding dropLimit option refs #22355
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    fd34cc77cd53fe8a6ff27d2be6d4d58bcd7adce3 Thu Nov 1 13:06:42 2018 -0700
    can also ouput dropLimit warning even when not dropping refs #22355
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    d50114fc351ec339453a18e928fac8ad2c6cf859 Thu Nov 1 13:23:24 2018 -0700
    need to place the option on the list refs #22355
• src/hg/hgTracks/cds.c
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    c04aef0e2bfd567e281ddd1af11b3e878ff4dde5 Wed Oct 31 15:27:53 2018 -0700
    Use hvGfxContrastingColor() instead of whiteIndex() for base coloring text so it's not invisible on light-colored PSL tracks.
• src/hg/hgTracks/hgTracks.h
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    f1464a78ed45c0f2c2c47112d5ec0585e875208e Tue Oct 30 15:01:29 2018 -0700
    some optimizations to speed up trackDb loads on huge hubs
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    f1464a78ed45c0f2c2c47112d5ec0585e875208e Tue Oct 30 15:01:29 2018 -0700
    some optimizations to speed up trackDb loads on huge hubs
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    a9d2eb19d6d3aef4e8a223466f1e0c3afd212973 Wed Oct 31 16:29:47 2018 -0700
    Fixing barChart hgc buffer overflow bug on sandboxes and genome-test, refs #18508
• src/hg/hgc/hgc.c
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    dc10667b65395ddad3445a55cd2a2c16a3715103 Fri Nov 2 15:10:20 2018 -0700
    Restricting use of tName in getAlignments query to doPslAltSeq only, after Braney pointed out in code review that changing the default behavior is not wise. refs CR #22353
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    7e53615be0552db123143b1fba66f0606db56699 Mon Oct 29 10:01:55 2018 -0700
    editing BLAT docs, refs #18992
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    6e784f9e7c3d402b626f7e6575c2f2d1ff4f5065 Tue Oct 30 09:16:52 2018 -0700
    changed date on newarch.html, editing newsarch.html & hgTracksHelp to 100char/line, additional word choice/grammer edits to newsarch.html, refs #22348
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 4, context: html, text, full: html, text
    cd4a69f99ad082b141bf918f77da6e5cbeab3606 Mon Oct 29 17:45:41 2018 -0700
    Doc new features. refs #21917
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 9, context: html, text, full: html, text
    2aff465bfebfc2c7a91f4f8371df42e0d52c86f2 Mon Oct 29 17:35:52 2018 -0700
    Add new interact track settings. refs #21917
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 9, context: html, text, full: html, text
    2aff465bfebfc2c7a91f4f8371df42e0d52c86f2 Mon Oct 29 17:35:52 2018 -0700
    Add new interact track settings. refs #21917
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    2aff465bfebfc2c7a91f4f8371df42e0d52c86f2 Mon Oct 29 17:35:52 2018 -0700
    Add new interact track settings. refs #21917
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 9, context: html, text, full: html, text
    6e784f9e7c3d402b626f7e6575c2f2d1ff4f5065 Tue Oct 30 09:16:52 2018 -0700
    changed date on newarch.html, editing newsarch.html & hgTracksHelp to 100char/line, additional word choice/grammer edits to newsarch.html, refs #22348
• src/hg/htdocs/images/GeneHancer_Announce.png
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    82b40fed7249000837669558ec04a79d49c46769 Fri Nov 2 11:27:16 2018 -0700
    Uploading a better image for the GH announcement ref#22048
• src/hg/htdocs/images/GeneHancer_Release.png
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    d6251dcc3f620540b9084eb05fffa68368dac2f2 Thu Nov 1 15:50:17 2018 -0700
    Uploading the image for GH release ref#22048
• src/hg/htdocs/indexNews.html
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    6e784f9e7c3d402b626f7e6575c2f2d1ff4f5065 Tue Oct 30 09:16:52 2018 -0700
    changed date on newarch.html, editing newsarch.html & hgTracksHelp to 100char/line, additional word choice/grammer edits to newsarch.html, refs #22348
• src/hg/inc/hdb.h
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    1c3d6739756883f6ac712e75eac7915a715545ef Sun Nov 4 15:03:42 2018 -0800
    Checking in new version 38 of refreshNamedSessionCustomTracks. I added the function setMinIndexLengthForTrashCleaner() to src/hg/lib/hdb.c since the trash cleaner will fail otherwise whenever you have a saved session with a custom track that is on a hub that is currently unavailable. Rather than risk losing the table in custom trash database, it needs to avoid this error and continue touching and running.
• src/hg/inc/trackDb.h
  • lines changed 35, context: html, text, full: html, text
    f1464a78ed45c0f2c2c47112d5ec0585e875208e Tue Oct 30 15:01:29 2018 -0700
    some optimizations to speed up trackDb loads on huge hubs
  • lines changed 1, context: html, text, full: html, text
    0689a6e26d5552dd64fdd4263985e1857236fd92 Wed Oct 31 12:21:17 2018 -0700
    enable view caching on native tracks
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    0689a6e26d5552dd64fdd4263985e1857236fd92 Wed Oct 31 12:21:17 2018 -0700
    enable view caching on native tracks
  • lines changed 16, context: html, text, full: html, text
    1c3d6739756883f6ac712e75eac7915a715545ef Sun Nov 4 15:03:42 2018 -0800
    Checking in new version 38 of refreshNamedSessionCustomTracks. I added the function setMinIndexLengthForTrashCleaner() to src/hg/lib/hdb.c since the trash cleaner will fail otherwise whenever you have a saved session with a custom track that is on a hub that is currently unavailable. Rather than risk losing the table in custom trash database, it needs to avoid this error and continue touching and running.
• src/hg/lib/hui.c
  • lines changed 48, context: html, text, full: html, text
    f1464a78ed45c0f2c2c47112d5ec0585e875208e Tue Oct 30 15:01:29 2018 -0700
    some optimizations to speed up trackDb loads on huge hubs
  • lines changed 10, context: html, text, full: html, text
    0689a6e26d5552dd64fdd4263985e1857236fd92 Wed Oct 31 12:21:17 2018 -0700
    enable view caching on native tracks
• src/hg/lib/trackDbCustom.c
  • lines changed 43, context: html, text, full: html, text
    f1464a78ed45c0f2c2c47112d5ec0585e875208e Tue Oct 30 15:01:29 2018 -0700
    some optimizations to speed up trackDb loads on huge hubs
  • lines changed 16, context: html, text, full: html, text
    0689a6e26d5552dd64fdd4263985e1857236fd92 Wed Oct 31 12:21:17 2018 -0700
    enable view caching on native tracks
• src/hg/makeDb/doc/hg19.txt
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    98604b63cbd9a753612467eae83a87271c940678 Wed Oct 31 07:54:35 2018 -0700
    continuing crispr 10K run after hive interruptions no redmine
• src/hg/makeDb/doc/hg38/miRnaAtlas.txt
  • lines changed 5, context: html, text, full: html, text
    44edc54639394583ef8f131a41161bbac8ffc661 Fri Nov 2 13:08:32 2018 -0700
    More improvements to miRna expression track: search, schema fixes, and column reordering, refs #18508
• src/hg/makeDb/genbank/etc/genbank-dbload
  • lines changed 2, context: html, text, full: html, text
    76dd77c5c1fec519ac155efbf776a417a76a7e0d Fri Nov 2 13:36:18 2018 -0700
    fix some comments per code review
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    448e6a0304e2f123bffe6fe91105065da9465146 Wed Oct 31 11:38:11 2018 -0700
    Adding ponAbe3 to hgwbeta.dbs, refs #20980
• src/hg/makeDb/trackDb/chicken/galGal6/chainNetvertebrate.ra
  • lines changed 3, context: html, text, full: html, text
    9275413658f0f5d6597b4e3f56fe285ee3291a10 Fri Nov 2 16:46:21 2018 -0700
    changing the default position and tracks for galGal6
• src/hg/makeDb/trackDb/chicken/galGal6/refSeqComposite.ra
  • lines changed 197, context: html, text, full: html, text
    9275413658f0f5d6597b4e3f56fe285ee3291a10 Fri Nov 2 16:46:21 2018 -0700
    changing the default position and tracks for galGal6
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    9275413658f0f5d6597b4e3f56fe285ee3291a10 Fri Nov 2 16:46:21 2018 -0700
    changing the default position and tracks for galGal6
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 4, context: html, text, full: html, text
    034522194d89c8e673aa5846e31ecfaf6799f63b Tue Oct 30 11:05:50 2018 -0700
    Updating http to https and replacing a broken link for fr3, uiLinks cronjob.
• src/hg/makeDb/trackDb/fugu/fr3/gold.html
  • lines changed 1, context: html, text, full: html, text
    034522194d89c8e673aa5846e31ecfaf6799f63b Tue Oct 30 11:05:50 2018 -0700
    Updating http to https and replacing a broken link for fr3, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 21, context: html, text, full: html, text
    e2f94af74afe8775b7b2b087f56ca3a1323a88bc Wed Oct 31 16:07:35 2018 -0700
    Changing Fix Patches track to yellow, vis pack and Alt Haplotypes alignment track to vis dense, per Jim. Changing existing patch/alt tracks in hg19 and hg38 to release beta,public. refs #18854
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    670305466a60eaf1461f36f803597d120f8c4384 Wed Oct 31 22:00:52 2018 -0700
    adding crispr 10K track no redmine
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
  • lines changed 27, context: html, text, full: html, text
    8a5a1b16415e4ad324e1355a8850ff93cfe16b43 Fri Nov 2 10:00:01 2018 -0700
    Updating the spacing to match our HTML guidelines, refs #21644
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    e7de1c97ffb7472a119373cd5b55969d4e040621 Fri Nov 2 10:10:27 2018 -0700
    Updating the HTML tags and attributes to use lower case characters, refs #21644
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    34ccda72e60349df74f64b6690dbeb61963beee5 Fri Nov 2 10:13:08 2018 -0700
    Fixing a broken link to the most recent GENCODE data, refs #21644
• src/hg/makeDb/trackDb/human/hg38/miRnaAtlas.html
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    03231a6501c91c1f05c367b31d3a010b59412e5a Tue Oct 30 12:36:02 2018 -0700
    Making requested changes to miRNA Atlas track, refs #18508
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    0cd049a27e0f807c253781805f822e58006fc335 Tue Oct 30 15:01:25 2018 -0700
    Fixing up tissue color orderings, good catch Dan, refs #18508
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    af49068253fd8b26e50d7b91a371964469969400 Wed Oct 31 13:48:27 2018 -0700
    Fixing tissue color table on description page for miRna atlas, refs #18508
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    638bbef2aaaa7e00387b7d7a44f070d80a273425 Thu Nov 1 12:14:44 2018 -0700
    Capitalized Tissue Atlas, changed word order, and replaced a comma with and, ref#18508
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
  • lines changed 5, context: html, text, full: html, text
    103d7a9648821063aca989ac90d982a459e825ed Tue Oct 30 11:49:22 2018 -0700
    Resolving duplicate wgRna stanzas, refs #21516
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    f477887c219ff0a9d8436a36911066c7d9521a48 Tue Oct 30 15:23:55 2018 -0700
    Fixing date on release pennantIcon ref#21516
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    e736115dbace5075e24e22f73675f8988e6aa4d3 Tue Oct 30 15:49:45 2018 -0700
    Fixing release tags in order to test on beta ref#21516
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    eab01a78141660eae06a09b3e69af061c6c7c866 Wed Oct 31 09:27:35 2018 -0700
    Removing stanza from old table to update miRBase data ref#21516
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    dbb87eeddadbbff5f1733f4716404519087ea48b Wed Oct 31 10:04:11 2018 -0700
    Removing release tag to update miRBase data on RR ref#21516
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 36, context: html, text, full: html, text
    03231a6501c91c1f05c367b31d3a010b59412e5a Tue Oct 30 12:36:02 2018 -0700
    Making requested changes to miRNA Atlas track, refs #18508
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    0cd049a27e0f807c253781805f822e58006fc335 Tue Oct 30 15:01:25 2018 -0700
    Fixing up tissue color orderings, good catch Dan, refs #18508
  • lines changed 1, context: html, text, full: html, text
    af52ad1b9302be072ddd3077d44a6b2e492fb6ee Wed Oct 31 07:42:49 2018 -0700
    Fixing capitalization in dataVersion string for miRna expression track, refs #18508
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    e2f94af74afe8775b7b2b087f56ca3a1323a88bc Wed Oct 31 16:07:35 2018 -0700
    Changing Fix Patches track to yellow, vis pack and Alt Haplotypes alignment track to vis dense, per Jim. Changing existing patch/alt tracks in hg19 and hg38 to release beta,public. refs #18854
  • lines changed 2, context: html, text, full: html, text
    ce943413af0ff49fbdb44bc7b32af24c48f12658 Thu Nov 1 17:04:17 2018 -0700
    Adding the beta release tag to the GENCODE v29 track for hg38, refs #21644
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    44edc54639394583ef8f131a41161bbac8ffc661 Fri Nov 2 13:08:32 2018 -0700
    More improvements to miRna expression track: search, schema fixes, and column reordering, refs #18508
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    159d7b87e4f2e4f91361f62f2f4506aba2bed8b2 Fri Nov 2 15:48:13 2018 -0700
    Removed release tags for miRNA track and publishing to RR
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    72f1edee42f1c3e3246bd2b05ac0cb9052e14db8 Fri Nov 2 16:18:33 2018 -0700
    Adding back release tags after noticing a buffer overflow on beta-public, ref #18505
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    afd24623cec4df065589e5bd85000b699763771b Fri Nov 2 16:22:04 2018 -0700
    Adding public release tags for beta-public, ref #18505
• src/hg/makeDb/trackDb/human/trackDb.ra
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    0596cf01ceba6c37d5d78196e973f0e10d34639b Wed Oct 31 10:54:32 2018 -0700
    Removing the include release tags from GH to release to RR ref#22048
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 5, context: html, text, full: html, text
    0648ac6449d121de2c8d39b5d8a6514ab45e3b78 Tue Oct 30 09:53:28 2018 -0700
    adding explaination for HGVS terminology to refSeqComposite.html, refs #22348
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    44edc54639394583ef8f131a41161bbac8ffc661 Fri Nov 2 13:08:32 2018 -0700
    More improvements to miRna expression track: search, schema fixes, and column reordering, refs #18508
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    e2f94af74afe8775b7b2b087f56ca3a1323a88bc Wed Oct 31 16:07:35 2018 -0700
    Changing Fix Patches track to yellow, vis pack and Alt Haplotypes alignment track to vis dense, per Jim. Changing existing patch/alt tracks in hg19 and hg38 to release beta,public. refs #18854
• src/hg/utils/phyloTrees/binaryTree.pl
  • lines changed 400, context: html, text, full: html, text
    f7857ed0961dd9e917726b780e5332be467161d7 Wed Oct 31 21:49:54 2018 -0700
    convert NCBI phylip polytomy trees to newick binary trees refs #22113
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • lines changed 33, context: html, text, full: html, text
    706db7af32b1c9847f2fa55c66f8936ef8b4936d Mon Oct 29 21:47:32 2018 -0700
    Fixing the problem with trash cleaner so that it always exits with non-zero value to indicate error clearly whenever the child process has exitCode greater than zero, gets killed by a timeout, or errAborts.
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    d0f49bd53aec0cda2217cf18ab7ebd30d2738191 Thu Nov 1 11:13:34 2018 -0700
    prefer to abort early for now rather than try to keep going. Especially this will allow error to pass up to the script that calls this.
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    ee556060739f9d32184c3fadf54ba3a14999a10c Sun Nov 4 14:13:09 2018 -0800
    Checking new version 37 of refreshNamedSessionCustomTracks. I explained importance of the program for future maintainers. I added a smaller incremental version number so that people can verify that the have the correct version, even if there are multiple versions being tested between releases. I renamed a misleading variable: childDone. I changed it to always produce exactly 10 children and split the list correctly between them. The previous version often made an extra child. By having it always produce the exact number of child forks requested, this allows the calling program to make one further verification that the program ran to completion by count the the number of messages from each child that exits normally.
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    1c3d6739756883f6ac712e75eac7915a715545ef Sun Nov 4 15:03:42 2018 -0800
    Checking in new version 38 of refreshNamedSessionCustomTracks. I added the function setMinIndexLengthForTrashCleaner() to src/hg/lib/hdb.c since the trash cleaner will fail otherwise whenever you have a saved session with a custom track that is on a hub that is currently unavailable. Rather than risk losing the table in custom trash database, it needs to avoid this error and continue touching and running.
• src/utils/gitTools/gilt
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    df7c3e757825d829e6573ce03d0559bc63327fb3 Thu Nov 1 01:57:12 2018 -0700
    fix gilt to handle wider pathnames. default 80 not long enough. do not like shorted paths with .../
• src/utils/qa/qaGbTracks
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    00b6bc62ac74afaee5bcc2a63a428721ab080afc Wed Oct 31 17:06:24 2018 -0700
    Making some minor changes to qa scripts, refs #20980 #22364
• src/utils/qa/weeklybld/buildEnv.csh
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    bb74bb4257be31e7db6efefa6bfee1fc70e0741d Mon Nov 5 09:57:29 2018 -0800
    v374 preview2, refs #22357

• lines changed: 1331
• files changed: 73