All File Changes

v336_base to v337_preview (2016-07-25 to 2016-08-01) v337

• confs/hgwbeta.hg.conf
  • lines changed 6, context: html, text, full: html, text
    28000694a5749f86b905d1b49b61832938ee050f Sun Jul 31 01:11:33 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    28000694a5749f86b905d1b49b61832938ee050f Sun Jul 31 01:11:33 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    28000694a5749f86b905d1b49b61832938ee050f Sun Jul 31 01:11:33 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/autoSql/LICENSE
  • lines changed 18, context: html, text, full: html, text
    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/hg/autoXml/LICENSE
  • lines changed 18, context: html, text, full: html, text
    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/hg/cirm/cdw/cdwCheckDataset/cdwCheckDataset.c
  • lines changed 2, context: html, text, full: html, text
    5800a214862f57bfbf06d92ce613f3558423d2e3 Fri Jul 29 13:32:53 2016 -0700
    Adding a print out of the wrangler value to the program
    
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 34, context: html, text, full: html, text
    26f820467afa323064eb88e948348545e9dc010b Fri Jul 29 14:31:08 2016 -0700
    Adding a "Download All" button to the CIRM CDW. No redmine.
    
• src/hg/cirm/cdw/cdwMakeContaminationQa/cdwMakeContaminationQa.c
  • lines changed 17, context: html, text, full: html, text
    829a8225ba4cd3d54afb68c55763cfa6ac1a914c Thu Jul 28 15:27:24 2016 -0700
    Adding in a polyA trim step before running BWA, refs 7334
    
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 18, context: html, text, full: html, text
    0dd9fe6d748b1908de30e74ed8b63a04db54e3f2 Thu Jul 28 15:16:14 2016 -0700
    adding in a trim step to the pairedEndQa validation step, refs #17334
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 3, context: html, text, full: html, text
    56e53f8d956070beb48dcf83ea3735a09062682c Fri Jul 29 13:19:59 2016 -0700
    Adding in a wrangler column to the cdwSubmit table to keep track of who submits what
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 280, context: html, text, full: html, text
    26f820467afa323064eb88e948348545e9dc010b Fri Jul 29 14:31:08 2016 -0700
    Adding a "Download All" button to the CIRM CDW. No redmine.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 12, context: html, text, full: html, text
    4abb3bf5c776ba0b89e6f83fe212952085b829fa Thu Jul 28 12:23:24 2016 -0700
    Adding in library file changes and makefile changes for cdwFlowCharts
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    56e53f8d956070beb48dcf83ea3735a09062682c Fri Jul 29 13:19:59 2016 -0700
    Adding in a wrangler column to the cdwSubmit table to keep track of who submits what
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 28, context: html, text, full: html, text
    b58525c691493b60efa96dc132d2e8cc0b242010 Thu Jul 28 15:26:44 2016 -0700
    Replacing the cutadapt call with Jim's new C program cdwFastqPolyFilter, refs #17334
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    4abb3bf5c776ba0b89e6f83fe212952085b829fa Thu Jul 28 12:23:24 2016 -0700
    Adding in library file changes and makefile changes for cdwFlowCharts
    
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    8ab4f2b62c360705e1630e3ed2da9396e89c38cc Wed Jul 27 16:13:07 2016 -0700
    Adding polya trimmer utility to makefile.
    
• src/hg/cirm/cdw/utils/cdwFastqPolyFilter/cdwFastqPolyFilter.c
  • lines changed 83, context: html, text, full: html, text
    78ae5c7d55c040ac5d0f3dc42bb04e559acbd57c Wed Jul 27 16:11:17 2016 -0700
    Making a little polyA trimmer for fastq files.
    
• src/hg/cirm/cdw/utils/cdwFastqPolyFilter/makefile
  • lines changed 3, context: html, text, full: html, text
    78ae5c7d55c040ac5d0f3dc42bb04e559acbd57c Wed Jul 27 16:11:17 2016 -0700
    Making a little polyA trimmer for fastq files.
    
• src/hg/hgApi/hgApi.c
  • lines changed 1, context: html, text, full: html, text
    cd70df9409f8b89c142bed7a7ee87a75c667a183 Wed Jul 27 15:35:04 2016 -0700
    always put track metadata on the HTML page (hidden by default) instead of requesting it
    through hgApi. This much more efficient because the browser already has
    the metadata when it's building the table #17790
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 17, context: html, text, full: html, text
    7cba4825e2cdac43466409afe3507dd7da0245c9 Fri Jul 22 17:15:46 2016 -0700
    Special handling for tables that happen to include the bin column in their autoSql (e.g. pgSnp tables and oreganno): disable bin unless user explicitly enables it, to match UI behavior. refs #17748
    
• src/hg/hgLogin/hgLogin.c
  • lines changed 8, context: html, text, full: html, text
    105193d3bc75ad4c8c5570cbd66286300c322bd3 Mon Jul 25 16:36:11 2016 -0700
    Always use https for hgLogin, even if returning to hgSession with http. refs #17778
    
  • lines changed 43, context: html, text, full: html, text
    53bfcc23b47e1dab4dc8d0aa7bc2ca5c121ced2b Tue Jul 26 12:28:12 2016 -0700
    hgLogin's links to itself and form posts to itself also need to use https, even if hgLogin was loaded via http (e.g. from a static page, bookmark, etc). refs #17778
    
  • lines changed 2, context: html, text, full: html, text
    d81a994fc5b713f0bafc32923e44d29c872c720b Fri Jul 29 16:18:55 2016 -0700
    Added a new hg.conf setting, login.https, so that mirror sites can turn off https for hgLogin if they don't support https (they really should). refs #17778 note-7
    
• src/hg/hgTracks/extTools.ra
  • lines changed 3, context: html, text, full: html, text
    481a1f2a2680f66d0e9948d9520ff8aaf6d9341b Thu Jul 28 10:37:34 2016 -0700
    changed http links over to https for NCBI in extTools.ra, refs #17793
    
• src/hg/hgc/hgc.c
  • lines changed 7, context: html, text, full: html, text
    04f51b90a6a1e3237013c7883e3e7d5ae3900a7b Fri Jul 22 14:45:10 2016 -0700
    Minor changes following code review, refs #17723
    
  • lines changed 1, context: html, text, full: html, text
    4aa7141dedea619f3bc7d42316f886bcfd554349 Thu Jul 28 20:30:09 2016 -0700
    Finishing touches on html-encoding of errors for warn/abort when using html output.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    77370fb299c80b3d6517432ec05a6dd91c240e6c Wed Jul 27 13:52:34 2016 -0700
    update doc on pennantIcon #17787
    
  • lines changed 7, context: html, text, full: html, text
    4f1b59a891e464d638bf4a37825f39452f0dc02f Wed Jul 27 17:12:47 2016 -0700
    adding docs for ${ $} $n and $taxId in track url, refs #17785
    
  • lines changed 7, context: html, text, full: html, text
    7d58900831ae0239429260f2c9646bfa2924a2ad Thu Jul 28 09:26:36 2016 -0700
    forgot to copy the doc to the url tag in last commit, refs #17785
    
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    af3e5802a955fa9aacd2d9fce65449f60805ab2e Wed Jul 27 11:32:06 2016 -0700
    Removing user survey from index page refs #17622
    
• src/hg/htdocs/license/index.html
  • lines changed 3, context: html, text, full: html, text
    6c7e138247d9282eb3dd9fb198c119a088002925 Wed Jul 27 15:58:27 2016 -0700
    adding the other two directories that belong in this list (per Jim)
    
  • lines changed 1, context: html, text, full: html, text
    884a3208878490c54863079d0cda6ae09f0d2c0c Wed Jul 27 16:22:02 2016 -0700
    more
    
• src/hg/inc/tablesTables.h
  • lines changed 12, context: html, text, full: html, text
    26f820467afa323064eb88e948348545e9dc010b Fri Jul 29 14:31:08 2016 -0700
    Adding a "Download All" button to the CIRM CDW. No redmine.
    
• src/hg/inc/wikiLink.h
  • lines changed 4, context: html, text, full: html, text
    d81a994fc5b713f0bafc32923e44d29c872c720b Fri Jul 29 16:18:55 2016 -0700
    Added a new hg.conf setting, login.https, so that mirror sites can turn off https for hgLogin if they don't support https (they really should). refs #17778 note-7
    
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    18322576ee363eb709c65697cc98be80ad1a2ad4 Thu Jul 28 11:15:44 2016 -0700
    fix problem with composite tracks with only one experiment in the matrix #17795
    
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    cd70df9409f8b89c142bed7a7ee87a75c667a183 Wed Jul 27 15:35:04 2016 -0700
    always put track metadata on the HTML page (hidden by default) instead of requesting it
    through hgApi. This much more efficient because the browser already has
    the metadata when it's building the table #17790
    
• src/hg/lib/annoStreamDb.c
  • lines changed 1, context: html, text, full: html, text
    3bae5ca22bf4695cff6eeb0988cc9708e1c83105 Mon Jul 25 12:20:15 2016 -0700
    Added missing SQL 'on' keyword -- triggered by joining snp147Mult with snp147ExceptionDesc (snp147Mult is a non-huge table and exceptions is comma-separated list).
    
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    4cfc3d3eb5486c004765de17570c548ea6c388d5 Thu Jul 28 18:13:22 2016 -0700
    Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    26f820467afa323064eb88e948348545e9dc010b Fri Jul 29 14:31:08 2016 -0700
    Adding a "Download All" button to the CIRM CDW. No redmine.
    
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    4aa7141dedea619f3bc7d42316f886bcfd554349 Thu Jul 28 20:30:09 2016 -0700
    Finishing touches on html-encoding of errors for warn/abort when using html output.
    
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    9d9d9d11bb623fc83f53140791f729890521ba63 Tue Jul 26 16:57:58 2016 -0700
    fix sorting problem with composites on hubs (cricket's list)
    
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    091248e1bd8c94faa0d5a732a9949616c1a7e50d Wed Jul 27 11:34:51 2016 -0700
    Wanted to make sure important information about hgc and substitutable url settings for item coordinates was not lost.
    
  • lines changed 10, context: html, text, full: html, text
    2db476e7f26a056f0a31ecd0ff8801d75e404a29 Wed Jul 27 12:12:47 2016 -0700
    changing meaning of ${ and $}, as suggested by Galt. Having some feeling
    this was used somewhere, but cannot find where right now. refs #17785
    
  • lines changed 28, context: html, text, full: html, text
    b0e2a9158cb1c7a90e60b8a79e2e27cbf6daa909 Wed Jul 27 13:36:48 2016 -0700
    allow pennantIcons to have URLs to the image #17787
    
  • lines changed 1, context: html, text, full: html, text
    cd70df9409f8b89c142bed7a7ee87a75c667a183 Wed Jul 27 15:35:04 2016 -0700
    always put track metadata on the HTML page (hidden by default) instead of requesting it
    through hgApi. This much more efficient because the browser already has
    the metadata when it's building the table #17790
    
• src/hg/lib/tablesTables.c
  • lines changed 45, context: html, text, full: html, text
    26f820467afa323064eb88e948348545e9dc010b Fri Jul 29 14:31:08 2016 -0700
    Adding a "Download All" button to the CIRM CDW. No redmine.
    
• src/hg/lib/wikiLink.c
  • lines changed 8, context: html, text, full: html, text
    105193d3bc75ad4c8c5570cbd66286300c322bd3 Mon Jul 25 16:36:11 2016 -0700
    Always use https for hgLogin, even if returning to hgSession with http. refs #17778
    
  • lines changed 23, context: html, text, full: html, text
    d81a994fc5b713f0bafc32923e44d29c872c720b Fri Jul 29 16:18:55 2016 -0700
    Added a new hg.conf setting, login.https, so that mirror sites can turn off https for hgLogin if they don't support https (they really should). refs #17778 note-7
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 22, context: html, text, full: html, text
    ca83404a952b1500d7bda386272dc5853b77895c Fri Jul 22 17:08:49 2016 -0700
    Updated snp147{,Common,Flagged,Mult,CodingDbSnp} after Chris Lee found incorrect assignment of cds-indel for noncoding transcripts. reds #17209 notes 25, 29-34, 37
    
  • lines changed 24, context: html, text, full: html, text
    1cfb2e9463729a67e65fe5ecab8a7c9fa20399be Mon Aug 1 10:04:02 2016 -0700
    Rebuilt snp147 tables in hg19 and hg38 after fixing incorrect function codes in table from dbSNP and re-running the pipeline from ucscFunc onward. refs #17209
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 23, context: html, text, full: html, text
    ca83404a952b1500d7bda386272dc5853b77895c Fri Jul 22 17:08:49 2016 -0700
    Updated snp147{,Common,Flagged,Mult,CodingDbSnp} after Chris Lee found incorrect assignment of cds-indel for noncoding transcripts. reds #17209 notes 25, 29-34, 37
    
  • lines changed 24, context: html, text, full: html, text
    1cfb2e9463729a67e65fe5ecab8a7c9fa20399be Mon Aug 1 10:04:02 2016 -0700
    Rebuilt snp147 tables in hg19 and hg38 after fixing incorrect function codes in table from dbSNP and re-running the pipeline from ucscFunc onward. refs #17209
    
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 2, context: html, text, full: html, text
    02d3713351304b52f88a3a2574b15e8bc9161ca6 Mon Jul 25 20:37:55 2016 -0700
    only align stuff that's destined for the RR.
    
• src/hg/makeDb/trackDb/uniprot.txt
  • lines changed 15, context: html, text, full: html, text
    4c393b4501da94c9c83efcf100c7b16e76464e01 Fri Jul 29 14:50:58 2016 -0700
    accidentally committed a text file
    
• src/hg/utils/automation/asmHubAssembly.pl
  • lines changed 117, context: html, text, full: html, text
    f9103716a0bdcae82d33a075098c7e45225ec636 Fri Jul 29 13:02:25 2016 -0700
    adding description pages refs #13553
    
• src/hg/utils/automation/asmHubCpG.pl
  • lines changed 142, context: html, text, full: html, text
    fc0750d7a420861f220d29233f6ecb8b87dbc0d5 Fri Jul 29 16:06:07 2016 -0700
    adding CpG description page refs #13553
    
• src/hg/utils/automation/asmHubGap.pl
  • lines changed 123, context: html, text, full: html, text
    445376e0fbda613dc5f9d0a4e29917bed5ceacb5 Fri Jul 29 11:29:08 2016 -0700
    constructing gap description page refs #13553
    
  • lines changed 2, context: html, text, full: html, text
    4a838fafbfebd353e1848856f68d1eaee1c47e19 Fri Jul 29 11:37:16 2016 -0700
    tweak formatting refs #13553
    
  • lines changed 5, context: html, text, full: html, text
    f9103716a0bdcae82d33a075098c7e45225ec636 Fri Jul 29 13:02:25 2016 -0700
    adding description pages refs #13553
    
• src/hg/utils/automation/asmHubHtml.pl
  • lines changed 1, context: html, text, full: html, text
    974e5d1403723e32a8f351e1a4698b8f87dd3ca3 Fri Jul 29 13:04:08 2016 -0700
    fixing reference to faCount.signature.txt file refs #13553
    
• src/hg/utils/automation/asmHubRmsk.pl
  • lines changed 181, context: html, text, full: html, text
    05b61ae39590ef963a47876444f1a7df2267fc24 Fri Jul 29 15:33:55 2016 -0700
    adding repeat masker description page refs #13553
    
• src/hg/utils/automation/asmHubSimpleRepeat.pl
  • lines changed 106, context: html, text, full: html, text
    03ff891a3a68d51d1954643ac3e2a735f01a6caa Mon Aug 1 09:25:08 2016 -0700
    adding simple repeats description refs #13553
    
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 53, context: html, text, full: html, text
    b1cb58ccc610a08237e6994c75d46fe4304aa6f6 Thu Jul 28 11:17:01 2016 -0700
    now including cpg island composite, window masker and all gaps refs #13553
    
  • lines changed 2, context: html, text, full: html, text
    f9103716a0bdcae82d33a075098c7e45225ec636 Fri Jul 29 13:02:25 2016 -0700
    adding description pages refs #13553
    
  • lines changed 1, context: html, text, full: html, text
    05b61ae39590ef963a47876444f1a7df2267fc24 Fri Jul 29 15:33:55 2016 -0700
    adding repeat masker description page refs #13553
    
  • lines changed 4, context: html, text, full: html, text
    fc0750d7a420861f220d29233f6ecb8b87dbc0d5 Fri Jul 29 16:06:07 2016 -0700
    adding CpG description page refs #13553
    
  • lines changed 2, context: html, text, full: html, text
    03ff891a3a68d51d1954643ac3e2a735f01a6caa Mon Aug 1 09:25:08 2016 -0700
    adding simple repeats description refs #13553
    
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 5, context: html, text, full: html, text
    f9103716a0bdcae82d33a075098c7e45225ec636 Fri Jul 29 13:02:25 2016 -0700
    adding description pages refs #13553
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 6, context: html, text, full: html, text
    90a463516b1e9e6b4b942dda675c607e5c4fccf6 Mon Jul 25 14:15:46 2016 -0700
    chmod * will lead to errors if there are files owned by other users -- so run chmod only on owned files.
    
  • lines changed 2, context: html, text, full: html, text
    bb05b8e2c72fe5abb64e506f75eaf612e57ad1a9 Fri Jul 29 14:42:26 2016 -0700
    Use HTTPS for NCBI. refs #17793
    
• src/hg/utils/automation/makefile
  • lines changed 8, context: html, text, full: html, text
    2e8514ae591dce68b477d63830f00a1a7d45afd0 Fri Jul 29 16:08:34 2016 -0700
    adding asmHub script files to the build refs #13553
    
  • lines changed 2, context: html, text, full: html, text
    5a1a3cdf1fc42cd842e06272245cccf4eb373b1a Sat Jul 30 07:50:40 2016 -0700
    fixed syntax error in makefile
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 147, context: html, text, full: html, text
    b53a2520706ff46e405ea364f91c92bd7ade3caa Wed Jul 27 15:31:20 2016 -0700
    Fixed problem with gff3ToGenePred where +1 and -1 translational
    frame shifts were not correctly encoded. This resulted in
    downstream CDS being frameshifted. This will split genePred exons
    blocks to allow correct representation.
    
    The output has been verified against the previous version
    of the program and all differences manually verified.
    
• src/hg/utils/gff3ToGenePred/tests/expected/frameShiftTest.gp
  • lines changed 8, context: html, text, full: html, text
    b53a2520706ff46e405ea364f91c92bd7ade3caa Wed Jul 27 15:31:20 2016 -0700
    Fixed problem with gff3ToGenePred where +1 and -1 translational
    frame shifts were not correctly encoded. This resulted in
    downstream CDS being frameshifted. This will split genePred exons
    blocks to allow correct representation.
    
    The output has been verified against the previous version
    of the program and all differences manually verified.
    
• src/hg/utils/gff3ToGenePred/tests/input/frameShifts.gff3
  • lines changed 79, context: html, text, full: html, text
    b53a2520706ff46e405ea364f91c92bd7ade3caa Wed Jul 27 15:31:20 2016 -0700
    Fixed problem with gff3ToGenePred where +1 and -1 translational
    frame shifts were not correctly encoded. This resulted in
    downstream CDS being frameshifted. This will split genePred exons
    blocks to allow correct representation.
    
    The output has been verified against the previous version
    of the program and all differences manually verified.
    
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    b53a2520706ff46e405ea364f91c92bd7ade3caa Wed Jul 27 15:31:20 2016 -0700
    Fixed problem with gff3ToGenePred where +1 and -1 translational
    frame shifts were not correctly encoded. This resulted in
    downstream CDS being frameshifted. This will split genePred exons
    blocks to allow correct representation.
    
    The output has been verified against the previous version
    of the program and all differences manually verified.
    
• src/inc/LICENSE
  • lines changed 18, context: html, text, full: html, text
    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/inc/htmshell.h
  • lines changed 3, context: html, text, full: html, text
    4cfc3d3eb5486c004765de17570c548ea6c388d5 Thu Jul 28 18:13:22 2016 -0700
    Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan
    
• src/lib/LICENSE
  • lines changed 18, context: html, text, full: html, text
    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/lib/htmshell.c
  • lines changed 13, context: html, text, full: html, text
    4cfc3d3eb5486c004765de17570c548ea6c388d5 Thu Jul 28 18:13:22 2016 -0700
    Fixes XSS for the early warning and abort messages. These were detected by system admins in Japan
    
  • lines changed 1, context: html, text, full: html, text
    f52636fabd76fcf998604f16d815cf606d52c758 Thu Jul 28 18:34:42 2016 -0700
    Reverting this line because it seems to cause unnecessary double-encoding of the error message.
    
  • lines changed 1, context: html, text, full: html, text
    4aa7141dedea619f3bc7d42316f886bcfd554349 Thu Jul 28 20:30:09 2016 -0700
    Finishing touches on html-encoding of errors for warn/abort when using html output.
    
• src/parasol/LICENSE
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    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/tagStorm/LICENSE
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    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/utils/LICENSE
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    271f311304ad01b5fd86f8f1e08a17a44e47323a Wed Jul 27 16:29:19 2016 -0700
    adding new LICENSES to the directories that are completely free (do not require a license). This is the MIT license and the wording has been approved by Jim.
    
• src/utils/makefile
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    5ee666862e4a3d2ef27c66f6b005b6349f29fb71 Wed Jul 27 16:13:32 2016 -0700
    Adding fastqStatsAndSubsample to utilities make.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    e34f8748f4fb875c3d1ff4d6e98767b109a3bf5d Mon Aug 1 10:19:43 2016 -0700
    v337 preview1
    

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