All File Changes

v367_preview2 to v367_base (2018-06-11 to 2018-06-18) v367

• src/hg/cirm/cdw/cdwQaAgent/cdwQaAgent
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    85f972c2206397cf73a9b08c08954639b8f0f325 Mon Jun 11 12:48:56 2018 -0700
    Moving cdwMakePairedEndQa to near end to reduce likelihood of race condition.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 7, context: html, text, full: html, text
    a228903c2915ce327f8239fd0f976a8a05b9cfd2 Wed Jun 13 15:27:23 2018 -0700
    Adding a noBackup option.
• src/hg/hgCustom/hgCustom.c
  • lines changed 6, context: html, text, full: html, text
    ac73ce04a776104b2cd6403fb59d95ba93711c22 Wed Jun 13 14:59:21 2018 -0700
    Add first cut user docs. Examples need a bit more work/testing. refs #21109
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 40, context: html, text, full: html, text
    1ce3327d3b999a7df4d636b24b44a449899dfd69 Mon Jun 11 10:33:48 2018 -0700
    barChart hgc draws a barGraph instead of boxplot when only one sample per category, refs #21548
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    7f2df21c4cd80508a8965db473f3d42d7ad0e8e1 Thu Jun 14 16:33:25 2018 -0700
    Fixing bar ordering bug for new bargraph hgc pages, refs #21548
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 14, context: html, text, full: html, text
    ac73ce04a776104b2cd6403fb59d95ba93711c22 Wed Jun 13 14:59:21 2018 -0700
    Add first cut user docs. Examples need a bit more work/testing. refs #21109
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    fa04fa22bcfdda936020eca1f4e3c6ce7bbfe0c8 Thu Jun 14 16:29:14 2018 -0700
    More references to new track type in user docs. refs #21615
• src/hg/htdocs/goldenPath/help/barChart.html
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    5f9daee34e972c2a46e51401a7ab2c439ebaec2e Wed Jun 13 12:19:22 2018 -0700
    barChart example 1: changed browser line coords to show all genes. added a line to show the names of the fields. changed primary names to gene names, making the ENS identifiers secondary. changed values to show a bit more variation among the peaks
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    fb483c1220bd8b644b99826d2ff5eca8136efe2a Wed Jun 13 12:32:42 2018 -0700
    barChart example 2: changed browser line to cover all three items
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 14, context: html, text, full: html, text
    fa04fa22bcfdda936020eca1f4e3c6ce7bbfe0c8 Thu Jun 14 16:29:14 2018 -0700
    More references to new track type in user docs. refs #21615
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 10, context: html, text, full: html, text
    fa04fa22bcfdda936020eca1f4e3c6ce7bbfe0c8 Thu Jun 14 16:29:14 2018 -0700
    More references to new track type in user docs. refs #21615
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 218, context: html, text, full: html, text
    ac73ce04a776104b2cd6403fb59d95ba93711c22 Wed Jun 13 14:59:21 2018 -0700
    Add first cut user docs. Examples need a bit more work/testing. refs #21109
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 38, context: html, text, full: html, text
    5d3ebd80940f480a813b59fa42d9eaa03a89c129 Wed Jun 13 15:40:53 2018 -0700
    Update trackDb docs for interact track type. refs #21109
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 66, context: html, text, full: html, text
    5d3ebd80940f480a813b59fa42d9eaa03a89c129 Wed Jun 13 15:40:53 2018 -0700
    Update trackDb docs for interact track type. refs #21109
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 42, context: html, text, full: html, text
    5d3ebd80940f480a813b59fa42d9eaa03a89c129 Wed Jun 13 15:40:53 2018 -0700
    Update trackDb docs for interact track type. refs #21109
• src/hg/htdocs/images/phylo/micMur3_3way.png
  • lines changed 0, context: html, text, full: html, text
    377405f8eb685657879db8eb6a19be5ccb0714c7 Thu Jun 14 16:02:39 2018 -0700
    for 3-way alignment on micMur3 no redmine
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    34d88003b0e7eccd3293db920077b7a3dfdd723b Thu Jun 14 16:15:23 2018 -0700
    incorrect item on top no redmine
• src/hg/inc/versionInfo.h
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    46c6b163494aff7c1726068b62418494b7fe9fe7 Mon Jun 18 10:18:33 2018 -0700
    New version number v367
• src/hg/lib/interact.as
  • lines changed 3, context: html, text, full: html, text
    ac73ce04a776104b2cd6403fb59d95ba93711c22 Wed Jun 13 14:59:21 2018 -0700
    Add first cut user docs. Examples need a bit more work/testing. refs #21109
• src/hg/makeDb/doc/balAcu1.txt
  • lines changed 68, context: html, text, full: html, text
    230b9662b6cad6121017880b076fd8d40fecc269 Wed Jun 13 11:06:40 2018 -0700
    add gold assembly search rule and lastz to hg38 refs #21583
• src/hg/makeDb/doc/equCab3/initialBuild.txt
  • lines changed 62, context: html, text, full: html, text
    6523ada01fa1e1a6e4167019b7cd63607609f20c Mon Jun 11 15:44:57 2018 -0700
    completed QA ready refs #21223
• src/hg/makeDb/doc/hg19.txt
  • lines changed 32, context: html, text, full: html, text
    d643ab2be2c1c54cf0daa4b84e914bb91d52dec8 Fri Jun 15 13:03:31 2018 -0700
    Adding exome tracks to gnomAD, refs #18951
• src/hg/makeDb/doc/hg19Patch13.txt
  • lines changed 153, context: html, text, full: html, text
    deb448760014f007f153baebb29f5a8007c3ed0b Mon Jun 11 10:06:10 2018 -0700
    adding patch13 to hg19 refs #9869
• src/hg/makeDb/doc/hg19PatchDescr.pl
  • lines changed 120, context: html, text, full: html, text
    deb448760014f007f153baebb29f5a8007c3ed0b Mon Jun 11 10:06:10 2018 -0700
    adding patch13 to hg19 refs #9869
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 14, context: html, text, full: html, text
    1f736c9167f033fa13f21da36d510d609bfa63e4 Mon Jun 11 10:40:23 2018 -0700
    adding chainNet to equCab3 refs #21223
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    83dfbdfee5e4c07370df74066e6f657df47250d0 Wed Jun 13 09:26:25 2018 -0700
    lastz chainNet to balAcu1 per user request refs #21583
• src/hg/makeDb/doc/micMur3/multiz3way.txt
  • lines changed 1416, context: html, text, full: html, text
    479634cda34febfcf8594e24f222d5e9cd6aa8ab Thu Jun 14 18:23:48 2018 -0700
    running up 3-way on micMur3 no redmine
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    b5a75fbe3b5f2ba9102e852c27161c880a39a0b3 Fri Jun 15 17:00:52 2018 -0700
    3-way alignment complete no redmine
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    66d0b28345df340070498839c4431bfaccc6e701 Fri Jun 15 17:01:33 2018 -0700
    3-way alignment complete no redmine
• src/hg/makeDb/doc/mm10.txt
  • lines changed 13, context: html, text, full: html, text
    1f736c9167f033fa13f21da36d510d609bfa63e4 Mon Jun 11 10:40:23 2018 -0700
    adding chainNet to equCab3 refs #21223
  • lines changed 75, context: html, text, full: html, text
    b203f2127214a1836d9db90028d65dece8482197 Thu Jun 14 12:07:12 2018 -0700
    add balAcu1 lastz chainNet refs #21583
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    29348bbbc35f924c98ed59b6781a67cd1773ce1a Wed Jun 13 13:53:48 2018 -0700
    add Angies patch maps to the haplotype psl for grchHg38
• src/hg/makeDb/outside/gtexAnalysis/README.txt
  • lines changed 1, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/buildNotes.transEqtl.txt
  • lines changed 17, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/filelist.txt
  • lines changed 5, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/gtexAnalysisHub.html
  • lines changed 9, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/gtexTransEqtl.html
  • lines changed 100, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/hg19/trackDb.ase.txt
  • lines changed 474, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/hg19/trackDb.eqtl.txt
  • lines changed 11, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/hg19/trackDb.txt
  • lines changed 462, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/outside/gtexAnalysis/hub/hub.txt
  • lines changed 1, context: html, text, full: html, text
    dcc86af8656c8726907e2989cbe7791289a26395 Thu Jun 14 16:26:18 2018 -0700
    Refine track description. Add track to GTEx analysis hub (full version was on test hub). Update build notes. refs #20546
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    723a5385f843cecfea3a840522bc5aa36b9b94be Wed Jun 13 10:25:49 2018 -0700
    adding gold/assembly search rule refs #21583
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
  • lines changed 4, context: html, text, full: html, text
    280e6ef919718e3ab1368d6ee5e2d579ec41b966 Fri Jun 15 07:43:10 2018 -0700
    Updating redirected links for bosTau6, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/gtexTranscExpr.html
  • lines changed 4, context: html, text, full: html, text
    7b88333e352f9509999f70bff2198c42e2b39b29 Wed Jun 13 15:00:24 2018 -0700
    Add link to Body Map HTML page. refs #18628
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    dbecb2fc91aa363d0a76b8e9416e340167de9ddc Mon Jun 11 10:51:03 2018 -0700
    added a hyphen
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    ade806d518d4bd01c62744d1155c13e112020d5f Fri Jun 15 13:14:21 2018 -0700
    Minor updates to gnomAD track html, refs #18951
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.html
  • lines changed 1065, context: html, text, full: html, text
    b6a4584ec8b42d2975e2fd81962d7d67506d42c8 Mon Jun 11 10:05:20 2018 -0700
    adding patch13 to hg19 refs #9869
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
  • lines changed 117, context: html, text, full: html, text
    b6a4584ec8b42d2975e2fd81962d7d67506d42c8 Mon Jun 11 10:05:20 2018 -0700
    adding patch13 to hg19 refs #9869
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    b6a4584ec8b42d2975e2fd81962d7d67506d42c8 Mon Jun 11 10:05:20 2018 -0700
    adding patch13 to hg19 refs #9869
  • lines changed 1, context: html, text, full: html, text
    9a00516aaec536418d63044db79ca438de78c260 Thu Jun 14 16:01:37 2018 -0700
    Adding beta release tag for gnomAD 2.0, refs #18951
  • lines changed 14, context: html, text, full: html, text
    01fe26e1e4ad15ae4e496ca88d17441e17ee9d64 Fri Jun 15 07:57:24 2018 -0700
    Adding the beta release tag to the missing gnomAD stanzas, refs #18951
  • lines changed 224, context: html, text, full: html, text
    d643ab2be2c1c54cf0daa4b84e914bb91d52dec8 Fri Jun 15 13:03:31 2018 -0700
    Adding exome tracks to gnomAD, refs #18951
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    f19221097f1eee55503c8d53a31423b2d3f1ecad Thu Jun 14 16:55:32 2018 -0700
    Changing miRna tissue atlas to a supertrack and changing the bar labels, refs #18508
• src/hg/makeDb/trackDb/marmoset/calJac3/bacEnds.html
  • lines changed 1, context: html, text, full: html, text
    80491f975de0c04cb836615380c3f257dbc46b13 Tue Jun 12 08:17:20 2018 -0700
    Updating links for calJac3, uiLinks cronjob.
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 8, context: html, text, full: html, text
    80491f975de0c04cb836615380c3f257dbc46b13 Tue Jun 12 08:17:20 2018 -0700
    Updating links for calJac3, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
  • lines changed 413, context: html, text, full: html, text
    2dda61d8163344f7a6f8c65a32e244431117f132 Fri Jun 15 16:33:03 2018 -0700
    adding 3-way conservation no redmine
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.3way.ra
  • lines changed 102, context: html, text, full: html, text
    2dda61d8163344f7a6f8c65a32e244431117f132 Fri Jun 15 16:33:03 2018 -0700
    adding 3-way conservation no redmine
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    c2210b6df23631c05b4725a60a4b3ff0c1b0bb75 Fri Jun 15 17:00:02 2018 -0700
    correct view limits on the phyloP track no redmine
• src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra
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    2dda61d8163344f7a6f8c65a32e244431117f132 Fri Jun 15 16:33:03 2018 -0700
    adding 3-way conservation no redmine
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
  • lines changed 59, context: html, text, full: html, text
    646b0caf1807041c0407418fb0fceca137078731 Wed Jun 13 11:15:44 2018 -0700
    adding Minke whale balAcu1 definitions refs #21583
• src/hg/utils/automation/doBlastzChainNet.pl
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    8fa409541ae77d8b6cd9bcc5bf5525f7a3f59502 Wed Jun 13 09:39:19 2018 -0700
    only use cluster hub for partition if blastzOutRoot option given, otherwise workhorse is the ticket refs #21583
• src/inc/srcVersion.h
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    46c6b163494aff7c1726068b62418494b7fe9fe7 Mon Jun 18 10:18:33 2018 -0700
    New version number v367
• src/test/buildTableDescriptions.pl
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    e77cadcbc61fd30f7498baf28439db07907184b4 Thu Jun 14 08:45:20 2018 -0700
    Adding test .as file to list of ignored files in buildTableDescriptions after email from Braney
• src/utils/cpgIslandExt/cpg_lh.c
  • lines changed 25, context: html, text, full: html, text
    3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700
    added information to usage output and add test example for inclusion in userApps refs #21617
• src/utils/cpgIslandExt/tests/expected.bed.gz
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    3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700
    added information to usage output and add test example for inclusion in userApps refs #21617
• src/utils/cpgIslandExt/tests/makefile
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    3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700
    added information to usage output and add test example for inclusion in userApps refs #21617
• src/utils/cpgIslandExt/tests/test.fa.gz
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    3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700
    added information to usage output and add test example for inclusion in userApps refs #21617
• src/utils/cpgIslandExt/tests/test.sh
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    3f4b90263d2006ff803d85c691aa7cecb973907d Thu Jun 14 10:45:54 2018 -0700
    added information to usage output and add test example for inclusion in userApps refs #21617
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/allOptions.output
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/extraFields.coords
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/extraFields.output
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/makefile
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/test.as
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/test.output
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/expMatrixToBarchartBed/tests/test.output2
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    bf8d339decb066765332e22f07ad320eda6c9d4d Wed Jun 13 17:08:27 2018 -0700
    Fixup of expMatrixToBarchartBed so barCharts can have extraFields and so the script works as stated in the barChart documentation, needed for miRna expression track, refs #18508
• src/utils/makefile
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    0d55c5beaf3c8c6f8b522959c49a57ec8800cde3 Thu Jun 14 10:46:33 2018 -0700
    adding cpgIslandExt to userApps refs #21617
• src/utils/qa/weeklybld/buildEnv.csh
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    7f20e528d9895bfc997b25cf28aa589b963fb7d4 Mon Jun 18 10:14:06 2018 -0700
    v367 final build, refs #21564

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• files changed: 78