All File Changes

v365_preview to v365_preview2 (2018-04-23 to 2018-04-30) v365

• src/hg/cirm/cdw/cdwFindSymlinkable/cdwFindSymlinkable.c
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    7491c3281db792dad6dd6e0516b0080c6bcb4d4b Mon Apr 23 17:29:53 2018 -0700
    Making cirm pipeline scanner handle resubmitted files better.
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    6c50cb8c924b5d9c95a898e653718596793a8011 Fri Apr 27 10:21:11 2018 -0700
    Support track hub names that contain '.' by first checking for '.hub_' in db.table.field strings. refs #21353
• src/hg/hgTables/gffOut.c
  • lines changed 12, context: html, text, full: html, text
    2452b8280ae2188283a2d158eebd8bc17a8ebdf5 Fri Apr 27 10:14:19 2018 -0700
    TB GFF output was assuming mysql db, failed on assembly hubs. refs #21353
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    3c52e3bc1b07eab603317f1c0f0801208197454a Tue Apr 24 16:35:43 2018 -0700
    Fix problem with output of interact track (yet another place that needs updating for new track types). refs #21109
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 4, context: html, text, full: html, text
    ddace43033d7cafd99731219a5ee6e203c64d6fb Thu Apr 26 11:02:30 2018 -0700
    Adding a note about searchIndex needing sorted input based on MLQ refs #15400
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    ddace43033d7cafd99731219a5ee6e203c64d6fb Thu Apr 26 11:02:30 2018 -0700
    Adding a note about searchIndex needing sorted input based on MLQ refs #15400
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    ddace43033d7cafd99731219a5ee6e203c64d6fb Thu Apr 26 11:02:30 2018 -0700
    Adding a note about searchIndex needing sorted input based on MLQ refs #15400
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    83351e1cc2eb41f62d03bdae2fd3fc4b269c364e Thu Apr 26 11:48:13 2018 -0700
    Fixing incorrect and missing dates for hgColleciton and NCBI RefSeq track announcements, no Redmine.
• src/hg/htdocs/gtexBodyMap.html
  • lines changed 1, context: html, text, full: html, text
    8f3eb53bbb79b3b4eb8d00ac4f53d03d7a3b15ea Thu Apr 26 16:16:36 2018 -0700
    18628
• src/hg/js/hgGtexTrackSettings.js
  • lines changed 13, context: html, text, full: html, text
    b06501353cfa1c73c4d8a2b5ff13cc021104088f Wed Apr 25 21:04:11 2018 -0700
    FF now seems to work w/o extra test (which broke Safari).
• src/hg/lib/customFactory.c
  • lines changed 21, context: html, text, full: html, text
    70ee68ec94d32ce657842aed1a25c65f69ebca14 Mon Apr 23 15:41:09 2018 -0700
    the custom track loaders were failing silently when not present refs #21330
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    3c52e3bc1b07eab603317f1c0f0801208197454a Tue Apr 24 16:35:43 2018 -0700
    Fix problem with output of interact track (yet another place that needs updating for new track types). refs #21109
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    21a59b0cdbfd27857b51632198a981faccf91113 Mon Apr 30 09:52:39 2018 -0700
    use sqlTableExists() in hTableExists for customTrash references, more efficient refs #21330
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    eb9622ef972f4e2b51d355a210d61defc2f64fcc Tue Apr 24 20:25:04 2018 -0700
    Fix table browser schema display for native track. refs #21109
• src/hg/lib/interact.as
  • lines changed 2, context: html, text, full: html, text
    8390fd6eea07493f2a92fa795dc08452c5087976 Tue Apr 24 15:08:01 2018 -0700
    Sanitize field description (bedToBigBed doesn't understand line-wraps. refs #21109
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    eb9622ef972f4e2b51d355a210d61defc2f64fcc Tue Apr 24 20:25:04 2018 -0700
    Fix table browser schema display for native track. refs #21109
• src/hg/lib/interact.c
  • lines changed 16, context: html, text, full: html, text
    eb9622ef972f4e2b51d355a210d61defc2f64fcc Tue Apr 24 20:25:04 2018 -0700
    Fix table browser schema display for native track. refs #21109
• src/hg/lib/joiner.c
  • lines changed 2, context: html, text, full: html, text
    6c50cb8c924b5d9c95a898e653718596793a8011 Fri Apr 27 10:21:11 2018 -0700
    Support track hub names that contain '.' by first checking for '.hub_' in db.table.field strings. refs #21353
• src/hg/makeDb/doc/hg19.txt
  • lines changed 94, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 110, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/doc/mm10.txt
  • lines changed 63, context: html, text, full: html, text
    ac5aa3a348ea06eb9e14762a7affc66bfcdb0d9e Wed Apr 25 10:55:55 2018 -0700
    mm10/oviAri4 chain net doc, refs #17247
  • lines changed 17, context: html, text, full: html, text
    89f6176ceb850ad98abdf610b628fa1503f33e56 Thu Apr 26 10:05:00 2018 -0700
    Steps to rerun lastz for mm10/oviAri4
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    e3ca4d83e5f6dac273754f3e6e1dbd551da4981f Fri Apr 27 10:27:29 2018 -0700
    Starting swap for mm10/oviAri4
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    a8e14b375134503a2f8e6c17aa656c9d3f16bfbe Fri Apr 27 11:13:57 2018 -0700
    Adding results of syntenic net featureBits to mm10/oviAri4, refs #17247
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    1d4793ea4a2df0d10ab4f25a2b74918105694f70 Fri Apr 27 11:46:08 2018 -0700
    Starting recip best after the swap finished, refs #17247
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    46aac13f8a4781c2616661f37573a9f95f151de7 Mon Apr 30 08:06:08 2018 -0700
    Done with recipbest for mm10/oviAri4, refs #17247
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    5f0f3b8d9d16b4999bf27d629b91daaaeefe510e Tue Apr 24 14:00:50 2018 -0700
    starting genbank updates for oviAri4/sheep refs #17247
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    84a22d80b4fce95191c9966c6ce9d5345cd6daae Mon Apr 23 15:31:54 2018 -0700
    don't build ccds for grcHhh38
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    5f0f3b8d9d16b4999bf27d629b91daaaeefe510e Tue Apr 24 14:00:50 2018 -0700
    starting genbank updates for oviAri4/sheep refs #17247
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    83897ed5a76bb0e7a08fa826a81b27d1f0f55b40 Wed Apr 25 19:54:04 2018 -0700
    missing required entry for oviAri4 in etc/genbank.conf
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    5f0f3b8d9d16b4999bf27d629b91daaaeefe510e Tue Apr 24 14:00:50 2018 -0700
    starting genbank updates for oviAri4/sheep refs #17247
• src/hg/makeDb/schema/all.joiner
  • lines changed 19, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
  • lines changed 9, context: html, text, full: html, text
    06774e95703e3e61767e5aeac2f41f3b8d3e987f Fri Apr 27 10:35:40 2018 -0700
    Adding oviAri4 to all.joiner, refs #17247
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 16, context: html, text, full: html, text
    019a227038abb584cc6f53bdb9c1c381b5723d45 Mon Apr 30 08:24:54 2018 -0700
    Getting sheep chain/nets into the right hg38 and mm10 composites, refs #17247
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    495ead9f30535c84f1b0cc43b53ab9908bdc6877 Fri Apr 20 16:08:03 2018 -0700
    Hiding the older GENCODE tracks (v27) for the newer dataset (v28), refs #21266
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.ra
  • lines changed 1, context: html, text, full: html, text
    495ead9f30535c84f1b0cc43b53ab9908bdc6877 Fri Apr 20 16:08:03 2018 -0700
    Hiding the older GENCODE tracks (v27) for the newer dataset (v28), refs #21266
• src/hg/makeDb/trackDb/human/snp151.html
  • lines changed 38, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/human/snp151.shared.html
  • lines changed 484, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/human/snp151Common.html
  • lines changed 28, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/human/snp151Flagged.html
  • lines changed 29, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/human/snp151Mult.html
  • lines changed 29, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 119, context: html, text, full: html, text
    5756dec7a00c540d5a1b5a9806ee7c598a07bde4 Tue Apr 17 12:37:08 2018 -0700
    snp151* tracks (dbSNP b151) for hg19 and hg38. refs #21010
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 16, context: html, text, full: html, text
    019a227038abb584cc6f53bdb9c1c381b5723d45 Mon Apr 30 08:24:54 2018 -0700
    Getting sheep chain/nets into the right hg38 and mm10 composites, refs #17247
• src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
  • lines changed 3, context: html, text, full: html, text
    cf121f0173c2427f67d8ccacb5d5f573e8781eba Tue Apr 24 11:20:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob for mm7.
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
  • lines changed 7, context: html, text, full: html, text
    cf121f0173c2427f67d8ccacb5d5f573e8781eba Tue Apr 24 11:20:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob for mm7.
• src/hg/makeDb/trackDb/mouse/mm7/picTar.html
  • lines changed 3, context: html, text, full: html, text
    cf121f0173c2427f67d8ccacb5d5f573e8781eba Tue Apr 24 11:20:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob for mm7.
• src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
  • lines changed 2, context: html, text, full: html, text
    cf121f0173c2427f67d8ccacb5d5f573e8781eba Tue Apr 24 11:20:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob for mm7.
• src/hg/makeDb/trackDb/mouse/rikenCageTc.html
  • lines changed 2, context: html, text, full: html, text
    cf121f0173c2427f67d8ccacb5d5f573e8781eba Tue Apr 24 11:20:03 2018 -0700
    Updating redirected links found by the uiLinks cronjob for mm7.
• src/hg/makeDb/trackDb/rhesus/refSeqAnno.html
  • lines changed 1, context: html, text, full: html, text
    82d0e1e79075adb11a2b452b86e808e759151bac Thu Apr 26 08:47:32 2018 -0700
    Updating redirected links for rheMac2, uiLinks cronjob
• src/hg/makeDb/trackDb/sheep/oviAri4/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    66352ae3358639042fb162edab5f1808f22151ff Fri Apr 27 11:17:23 2018 -0700
    Adding gold table search rule fixup for oviAri4, refs #17247
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
  • lines changed 59, context: html, text, full: html, text
    019a227038abb584cc6f53bdb9c1c381b5723d45 Mon Apr 30 08:24:54 2018 -0700
    Getting sheep chain/nets into the right hg38 and mm10 composites, refs #17247
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
  • lines changed 1, context: html, text, full: html, text
    c9a89085e2c590490f2207ef73609ae8fb3298e5 Thu Apr 26 14:33:42 2018 -0700
    Updating a broken link on the All GENCODE track description page, refs #21266
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    5dc6b6b09489899acac644dea091f5d1ae9916d3 Fri Apr 27 13:39:04 2018 -0700
    Updating the CNIO link as per Mark's suggestion, refs #21266
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 8, context: html, text, full: html, text
    a57e40ceedc46023800935b5a041a842ba004f74 Fri Apr 27 08:43:22 2018 -0700
    Updating redirected links for danRer7, uiLinks cronjob.
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 2, context: html, text, full: html, text
    a57e40ceedc46023800935b5a041a842ba004f74 Fri Apr 27 08:43:22 2018 -0700
    Updating redirected links for danRer7, uiLinks cronjob.
• src/hg/makeDb/trackDb/zebrafish/danRer7/gold.html
  • lines changed 3, context: html, text, full: html, text
    a57e40ceedc46023800935b5a041a842ba004f74 Fri Apr 27 08:43:22 2018 -0700
    Updating redirected links for danRer7, uiLinks cronjob.
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 3, context: html, text, full: html, text
    50db0a2de106608b779d58a815be51eb7df4f1c8 Wed Apr 25 17:25:57 2018 -0700
    fix syntenicNet scripting refs #18874
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 21, context: html, text, full: html, text
    a007cb8656504258c3815df9175f6cd37f1eba6c Thu Apr 26 11:04:08 2018 -0700
    Update doDbSnp.pl tryToMakeLiftUpFromNcbiAssemblyReportFile to use latest _alt-style naming and also support _fix.
• src/hg/utils/automation/verifyBrowser.pl
  • lines changed 1, context: html, text, full: html, text
    bf6083391c5578cf6fa5a037a0d18a5c1bc9b4a4 Fri Apr 27 13:47:10 2018 -0700
    all.joiner should be checked in usr/local/apache/cgi-bin/all.joiner refs #17247
• src/inc/common.mk
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    bb5e95e9e94531c071c2a5e89da5ac2e654c7047 Mon Apr 23 17:03:25 2018 -0700
    Changes with Galt to allow getting -Werror on the CIRM machines. This makes the make variable about hgwdev more explicit
  • lines changed 4, context: html, text, full: html, text
    8ba547a2a42aa8d00d6cdf52f8d5fff5bff68b3a Mon Apr 23 17:20:34 2018 -0700
    allow error-handling (stop on error) for cirm-01. make will behave more reliably with warnings and errors.
• src/utils/qa/weeklybld/buildEnv.csh
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    4b63759d1a2119fac1ec8a3b4347c94e936ba1bd Mon Apr 30 09:59:47 2018 -0700
    v365 preview2 refs #21332
• src/utils/qa/weeklybld/doZip.csh
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    b782f3da841af1ff22af883f1ef0f2a9457deab4 Mon Apr 23 22:33:12 2018 -0700
    temporary comment out copies to hgdownload-sd while it is off line no redmine
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 4, context: html, text, full: html, text
    b782f3da841af1ff22af883f1ef0f2a9457deab4 Mon Apr 23 22:33:12 2018 -0700
    temporary comment out copies to hgdownload-sd while it is off line no redmine
• src/utils/qa/weeklybld/userApps.sh
  • lines changed 4, context: html, text, full: html, text
    b782f3da841af1ff22af883f1ef0f2a9457deab4 Mon Apr 23 22:33:12 2018 -0700
    temporary comment out copies to hgdownload-sd while it is off line no redmine

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• files changed: 65