All File Changes

v347_preview2 to v347_base (2017-03-27 to 2017-04-03) v347

• src/hg/hgc/hgc.c
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    347ccb4b97cc6262b17f951a97f0eb49f81d8a04 Tue Mar 28 13:49:21 2017 -0700
    may as well use the string that has been carefully constructed refs #19079
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    ab0e825a8d803a2fe12374a6ed834199080ab109 Fri Mar 31 23:49:25 2017 -0700
    don't do fancy indel display with custom blat tracks
• src/hg/htdocs/training/index.html
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    10a548dd0d284b86848a3d4ed93d3207987f3179 Wed Mar 29 15:21:14 2017 -0700
    adding another Texas workshop
• src/hg/inc/ncbiRefSeqOther.as
  • lines changed 36, context: html, text, full: html, text
    3aa8f8f910395a46660ba59d42987df23fc6a453 Wed Mar 29 14:18:10 2017 -0700
    recording the schema for ncbiRefSeqOther extended bigBed schema refs #13673
• src/hg/inc/versionInfo.h
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    d53b61de2752fd4bc6995101d47eaa8ab7e697aa Mon Apr 3 09:52:29 2017 -0700
    New version number v347
• src/hg/js/hgTracks.js
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    45ad3b560f9084749cfd2619035b6ed4e0f56c63 Fri Mar 31 16:29:21 2017 -0700
    fixing refs #19170
• src/hg/makeDb/crisprTrack/createBigBed.py
  • lines changed 16, context: html, text, full: html, text
    85d047eb1841eae8c6c2ee393d3ff98a5533817a Wed Mar 29 17:40:42 2017 -0700
    fixing the crispr track script after a bug report from Angela Brooks, no redmine (and will probably entail a re-push of all crispr tracks on all 10 or so assemblies)
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 223, context: html, text, full: html, text
    a056181e5d871edab02c67feb42c3951b42e808d Fri Mar 31 00:26:03 2017 -0700
    lastz chainNet runs for rhiBie1 xenTro9 xenLae2 refs #18958 #19151 #17435
• src/hg/makeDb/doc/manPen1/initialBuild.txt
  • lines changed 19, context: html, text, full: html, text
    93b3630bbcacbdefacda25f40c6a785f54b5a766 Mon Mar 27 14:51:38 2017 -0700
    adding gold table search rule refs #15515
• src/hg/makeDb/doc/mm10.txt
  • lines changed 129, context: html, text, full: html, text
    89710b2afec0e248b15d4080bf114d44ce8181b2 Fri Mar 31 00:18:34 2017 -0700
    working up xenTro9 and xenLae2 lastz chainNet tracks refs #17435 #19151
• src/hg/makeDb/doc/tupChi1/initialBuild.txt
  • lines changed 24, context: html, text, full: html, text
    29b3b8c536e52c763eaac9c322ee474c2ce06240 Fri Mar 31 00:27:30 2017 -0700
    tupChi1 done and QA Ready refs #10146
• src/hg/makeDb/doc/tupChi1/lastzRuns.txt
  • lines changed 207, context: html, text, full: html, text
    4c3dab38b41e4385028dc2f7ee0f76c8c3c2a9f5 Fri Mar 31 00:30:32 2017 -0700
    lastz chainNet runs for galVar1 hg19 hg38 mm10 tupBel1 refs #10146
• src/hg/makeDb/doc/tupChi1/multiz4way.txt
  • lines changed 1461, context: html, text, full: html, text
    f0e2998a468ec328f3336cde01a4e1b9e3273e59 Tue Mar 28 10:25:20 2017 -0700
    working up a small 4-way for Juergen refs #10146
  • lines changed 39, context: html, text, full: html, text
    45ea203bc940e6218145977baa26078b8f6e11ca Tue Mar 28 12:06:03 2017 -0700
    4-way downloads done refs #10146
• src/hg/makeDb/doc/xenLae2/initialBuild.txt
  • lines changed 843, context: html, text, full: html, text
    18ff13be4175cd7e95e106752e59bf66272e3a7f Wed Mar 29 14:51:26 2017 -0700
    masked sequence available refs #17435
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    3e681caf6447b2a59eef2ca7d0ddee3d7f9bfa15 Thu Mar 30 16:26:01 2017 -0700
    starting genbank run refs #17435
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    3510e8852c6a43c649aa82f1e62896d2820f7066 Fri Mar 31 00:17:25 2017 -0700
    running up genbank refs #17435
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 14, context: html, text, full: html, text
    124eb6aa179a7b46d7715bf0bd1cd666c7819cd4 Fri Mar 31 00:19:52 2017 -0700
    liftover to xenTro9 refs #19151
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 14, context: html, text, full: html, text
    b78a4f9c10e1ba98096be2db6c352f6905d1d44e Fri Mar 31 00:20:36 2017 -0700
    liftover to xenTro9 refs #19151
• src/hg/makeDb/doc/xenTro9/initialBuild.txt
  • lines changed 820, context: html, text, full: html, text
    558172af273129615a2adbae6c8d8862404b3d4d Mon Mar 27 13:26:12 2017 -0700
    starting xenTro9 browser build refs #19151
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    63543032e4482a8073eeda5973dc8d47dfe218f2 Fri Mar 31 00:16:03 2017 -0700
    working through more lastz chainNet runs refs #19151
• src/hg/makeDb/doc/xenTro9/lastzRuns.txt
  • lines changed 56, context: html, text, full: html, text
    63543032e4482a8073eeda5973dc8d47dfe218f2 Fri Mar 31 00:16:03 2017 -0700
    working through more lastz chainNet runs refs #19151
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    27fda4ff70c44812f24c5b3f70a6b712996d3882 Wed Mar 29 10:04:24 2017 -0700
    adding xenTro9 to the update alignments refs #19151
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 21, context: html, text, full: html, text
    25c631fc8b79b34d3db19c482a979c16360c21f7 Tue Mar 28 10:18:44 2017 -0700
    adding xenTro9 X, tropicalis refs #19151
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    a6a3a94f8e616b6ba0193cc3ffd894283e08d715 Thu Mar 30 16:22:56 2017 -0700
    Added xenLae Xenopus laevis refs #17435
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    27fda4ff70c44812f24c5b3f70a6b712996d3882 Wed Mar 29 10:04:24 2017 -0700
    adding xenTro9 to the update alignments refs #19151
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    a6a3a94f8e616b6ba0193cc3ffd894283e08d715 Thu Mar 30 16:22:56 2017 -0700
    Added xenLae Xenopus laevis refs #17435
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    7b3800545b5c348f619b01a73847cf219f71da48 Wed Mar 29 10:19:09 2017 -0700
    adding xenTro9 rules refs #19151
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    5602ba37bef06187a16bbdf64740c07f72c515f5 Thu Mar 30 12:10:28 2017 -0700
    adding xenLae2 rules refs #17435
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 3, context: html, text, full: html, text
    0ffea07151f44eb7bbc08122f391db333c1b06ea Thu Mar 30 14:13:45 2017 -0700
    documenting the PAM thin bar for all crispr tracks, refs #19167
• src/hg/makeDb/trackDb/drosophila/droSim2/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    f6396fe6bbab0048bff8d20952fc4cbb06e47eef Thu Mar 30 13:50:32 2017 -0700
    adding chainNet overrides refs #14560
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    f6396fe6bbab0048bff8d20952fc4cbb06e47eef Thu Mar 30 13:50:32 2017 -0700
    adding chainNet overrides refs #14560
• src/hg/makeDb/trackDb/human/hg19/crispr.html
  • lines changed 3, context: html, text, full: html, text
    c26ecddb046ef70332149e3668d1218ed67169eb Mon Apr 3 09:27:18 2017 -0700
    Adding new documentation lines to hg19 and hg38 specific crispr track descriptions, refs #19167
• src/hg/makeDb/trackDb/human/hg38/crispr.html
  • lines changed 3, context: html, text, full: html, text
    c26ecddb046ef70332149e3668d1218ed67169eb Mon Apr 3 09:27:18 2017 -0700
    Adding new documentation lines to hg19 and hg38 specific crispr track descriptions, refs #19167
• src/hg/makeDb/trackDb/macaca/macNem1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700
    adding xenTro9 to the build refs #19151
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    d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700
    adding xenLae2/frog to the build refs #17435
• src/hg/makeDb/trackDb/micOch/micOch1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/pangolin/manPen1/trackDb.ra
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    2ff2df7e6108aa43be643a90608349fc04607200 Mon Mar 27 14:49:57 2017 -0700
    add search rule for gold table refs #15515
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/trackDb.ra
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    033265743249247f933e7302af452ff9f6be0274 Wed Mar 29 13:00:20 2017 -0700
    changing visibility for snp(147) track on galGal5 to dense
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
  • lines changed 427, context: html, text, full: html, text
    9e09a1d7d6dd7c108c30c580ba5a9631a37fb0c8 Tue Mar 28 11:59:12 2017 -0700
    adding 4-way alignment refs #10146
• src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.4way.ra
  • lines changed 102, context: html, text, full: html, text
    9e09a1d7d6dd7c108c30c580ba5a9631a37fb0c8 Tue Mar 28 11:59:12 2017 -0700
    adding 4-way alignment refs #10146
• src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    9e09a1d7d6dd7c108c30c580ba5a9631a37fb0c8 Tue Mar 28 11:59:12 2017 -0700
    adding 4-way alignment refs #10146
• src/hg/makeDb/trackDb/whale/orcOrc1/description.html
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/xenTro/xenLae2/description.html
  • lines changed 64, context: html, text, full: html, text
    d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700
    adding xenLae2/frog to the build refs #17435
• src/hg/makeDb/trackDb/xenTro/xenLae2/gap.html
  • lines changed 30, context: html, text, full: html, text
    d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700
    adding xenLae2/frog to the build refs #17435
• src/hg/makeDb/trackDb/xenTro/xenLae2/gold.html
  • lines changed 34, context: html, text, full: html, text
    d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700
    adding xenLae2/frog to the build refs #17435
• src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700
    adding xenLae2/frog to the build refs #17435
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    e5d119653130ef7319d517fbd9cd402fbc5146ed Thu Mar 30 12:48:21 2017 -0700
    adding gold track search rule resf #17435
• src/hg/makeDb/trackDb/xenTro/xenTro9/description.html
  • lines changed 64, context: html, text, full: html, text
    a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700
    adding xenTro9 to the build refs #19151
  • lines changed 1, context: html, text, full: html, text
    e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700
    fixup biosample reference refs #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/gap.html
  • lines changed 30, context: html, text, full: html, text
    a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700
    adding xenTro9 to the build refs #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/gold.html
  • lines changed 34, context: html, text, full: html, text
    a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700
    adding xenTro9 to the build refs #19151
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700
    adding xenTro9 to the build refs #19151
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    22341ea540b0cfb603995bc2897e9e0655848977 Mon Mar 27 14:54:55 2017 -0700
    adding gold table search rule refs #19151
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    2fafa17e1e857dbf37a65ec4ccd721b6c3d7d7d5 Mon Mar 27 13:48:24 2017 -0700
    need to have trackDb.chainNet.other.ra present refs #19151
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    8b48f7cfea69513a415605c9672c0d43982df8b3 Tue Mar 28 10:00:22 2017 -0700
    fixup biosample reference refs #19151
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 48, context: html, text, full: html, text
    134ff01a30e6a4407f0b0271536d15e82d6fd8fd Tue Mar 28 16:46:35 2017 -0700
    finally adding the clinvar star rating to our bigBed file, refs #17970
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 3, context: html, text, full: html, text
    134ff01a30e6a4407f0b0271536d15e82d6fd8fd Tue Mar 28 16:46:35 2017 -0700
    finally adding the clinvar star rating to our bigBed file, refs #17970
• src/hg/utils/phyloTrees/209way.nh
  • lines changed 9, context: html, text, full: html, text
    050b84cd063f57788bf9756b825331c7fdba6d50 Thu Mar 30 14:39:21 2017 -0700
    adjusting distances to equal the 191way refs #17545
• src/hg/utils/phyloTrees/213way.commonNames.nh
  • lines changed 213, context: html, text, full: html, text
    dff685504119eaadc1d7c1aeae0eca7499fb6cd7 Thu Mar 30 15:43:25 2017 -0700
    adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
• src/hg/utils/phyloTrees/213way.nh
  • lines changed 213, context: html, text, full: html, text
    9b912a13bff7b8f4066ed24e821d0592619e45c1 Thu Mar 30 15:25:49 2017 -0700
    adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
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    dff685504119eaadc1d7c1aeae0eca7499fb6cd7 Thu Mar 30 15:43:25 2017 -0700
    adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
• src/hg/utils/phyloTrees/213way.scientificNames.nh
  • lines changed 213, context: html, text, full: html, text
    dff685504119eaadc1d7c1aeae0eca7499fb6cd7 Thu Mar 30 15:43:25 2017 -0700
    adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
• src/inc/net.h
  • lines changed 3, context: html, text, full: html, text
    8bb6e8cc14b264b4a32b855045151e98638267c3 Tue Mar 28 23:12:00 2017 -0700
    Step1 Seven Bridges HIPAA-compliant Amazon Storage securely signed URLs meant for GET do not allow them to be used with another method such as HEAD. Therefore we use a GET with byterange=0-0 so that it will still work with Amazon and still return correct info about size and last-modified date of the bigDataUrl file. refs #19158
• src/lib/https.c
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    366ddf93550ccfa3a4b122f3df88429ced4db32d Thu Mar 30 21:22:13 2017 -0700
    oops. conditional comp version needs to match parameters.
• src/lib/net.c
  • lines changed 20, context: html, text, full: html, text
    8bb6e8cc14b264b4a32b855045151e98638267c3 Tue Mar 28 23:12:00 2017 -0700
    Step1 Seven Bridges HIPAA-compliant Amazon Storage securely signed URLs meant for GET do not allow them to be used with another method such as HEAD. Therefore we use a GET with byterange=0-0 so that it will still work with Amazon and still return correct info about size and last-modified date of the bigDataUrl file. refs #19158
• src/lib/udc.c
  • lines changed 1, context: html, text, full: html, text
    6ad1af3fffe90d3fc367fc39bb226d6137851b50 Mon Mar 27 15:53:56 2017 -0700
    adding udc fix so we can load signed URLs from Amazon S3, refs #18989
  • lines changed 17, context: html, text, full: html, text
    8bb6e8cc14b264b4a32b855045151e98638267c3 Tue Mar 28 23:12:00 2017 -0700
    Step1 Seven Bridges HIPAA-compliant Amazon Storage securely signed URLs meant for GET do not allow them to be used with another method such as HEAD. Therefore we use a GET with byterange=0-0 so that it will still work with Amazon and still return correct info about size and last-modified date of the bigDataUrl file. refs #19158
• src/product/minimal.hg.conf
  • lines changed 2, context: html, text, full: html, text
    40bc7c01859aa18d80ba7bb742ee9c97e74c2058 Tue Mar 28 14:11:00 2017 -0700
    Adding trackDb line to example minimal.hg.conf so command line can work on mirrors, gbib has this setting by default. Also uncommenting mysql socket line because the path differs for various systems, refs #12216
• src/product/mirrorDocs/staticPage.lua
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    e100240b15374bcaf40ffc1edf336369823df459 Mon Mar 27 14:20:23 2017 -0700
    Deleting commented out lines as per code review, refs #19147
• src/utils/apacheLogParse
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    b22d8bfdf6dd0e96f0aab149fa505dfa4392ee08 Wed Mar 29 17:38:53 2017 -0700
    writing out bot IP addresses for Matt's new log analysis scripts, no redmine
• src/utils/bedJoinTabOffset
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    33efa29f7bf07da99da316e6228ad86957bf760b Wed Mar 29 12:11:54 2017 -0700
    adding bedJoinTabOffset tool, for new track type by Kate, no redmine
• src/utils/makefile
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    33efa29f7bf07da99da316e6228ad86957bf760b Wed Mar 29 12:11:54 2017 -0700
    adding bedJoinTabOffset tool, for new track type by Kate, no redmine
• src/utils/qa/getRRdatabases.csh
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    ddd04f80fbc63b2feabf84f335fbb999f6247200 Thu Mar 30 08:01:05 2017 -0700
    changing table dump location, no redmine
• src/utils/qa/getRRdumpfile.csh
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    ddd04f80fbc63b2feabf84f335fbb999f6247200 Thu Mar 30 08:01:05 2017 -0700
    changing table dump location, no redmine
• src/utils/qa/getRRtables.csh
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    ddd04f80fbc63b2feabf84f335fbb999f6247200 Thu Mar 30 08:01:05 2017 -0700
    changing table dump location, no redmine
• src/utils/qa/updateTimes.csh
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    5d45c47b42a0621db9fba255d08a0e9f3257848d Thu Mar 30 09:01:13 2017 -0700
    Correcting minor mistake in output by adding extra space, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    3a03cd6b8c2449cc1ddaa2834b5e1c77b03e796f Mon Apr 3 09:38:00 2017 -0700
    v347 final build refs #19120

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• files changed: 84