All File Changes

v348_base to v349_preview (2017-04-24 to 2017-05-01) v349

• .gitignore
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    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• confs/hgwdev.hg.conf
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    367d6fc0aab2c949a13aa72c8aa0fdcfa68a11b6 Sun Apr 30 01:11:28 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 2, context: html, text, full: html, text
    b5ee46a6dd9ae05c81783d6eff6e3fa72d4e29b3 Tue Apr 25 09:47:30 2017 -0700
    more fallout from moving a readAndIgnore routine to obscure.c
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    c6a614318907209179dfefa774efefd74e3671f8 Tue Apr 25 15:11:52 2017 -0700
    adding strong reference to Track Hubs on Custom Track pages. refs #19301
• src/hg/hgGeneGraph/README.txt
  • lines changed 13, context: html, text, full: html, text
    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 1951, context: html, text, full: html, text
    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
  • lines changed 38, context: html, text, full: html, text
    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/hgGeneGraph/makefile
  • lines changed 35, context: html, text, full: html, text
    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/hg/hgLogin/hgLogin.c
  • lines changed 26, context: html, text, full: html, text
    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/hg/hgSession/hgSession.c
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    87163e46373817c4237d5091b5910e07f0456057 Mon Apr 24 15:22:13 2017 -0700
    hgSession can now find convert on GBiB
• src/hg/hgTracks/config.c
  • lines changed 25, context: html, text, full: html, text
    71b6403f90f9f221004a07cbd4e5aecedd9f6438 Mon Apr 24 12:41:27 2017 -0700
    Refs #17538. Adds ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an on-line server. It still supports the URL through UDC however, which is more efficient for large custom region lists and also provides backwards compatibility. Uses sha1 instead of md5 for faster speed now.
• src/hg/hgTracks/hgTracks.c
  • lines changed 158, context: html, text, full: html, text
    71b6403f90f9f221004a07cbd4e5aecedd9f6438 Mon Apr 24 12:41:27 2017 -0700
    Refs #17538. Adds ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an on-line server. It still supports the URL through UDC however, which is more efficient for large custom region lists and also provides backwards compatibility. Uses sha1 instead of md5 for faster speed now.
  • lines changed 5, context: html, text, full: html, text
    a3c54789f08140d5c91b7d3c011a6fc9b967560f Mon Apr 24 14:56:51 2017 -0700
    Add a little touch to keep sha1 from the trash cleaner. refs #17358
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    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
  • lines changed 2, context: html, text, full: html, text
    08192e6c87c63c4e0c9e448846dd7f195af73c88 Wed Apr 26 14:26:02 2017 -0700
    shift from name sha1 to rSha1 to avoid link problems with openssl.
  • lines changed 6, context: html, text, full: html, text
    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/hg/hgVai/hgVai.c
  • lines changed 18, context: html, text, full: html, text
    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/hgc/barChartClick.c
  • lines changed 25, context: html, text, full: html, text
    41d01fd0f045a58696edb753981feef6865f62e5 Mon Apr 24 15:11:24 2017 -0700
    1. Fix schema file syntax problem, strangely in comment. Caused crash in QA testing. 2. Allow bigBarChart w/o offset/len into matrix. refs #18736
  • lines changed 3, context: html, text, full: html, text
    ad2f4709ca23e0f117c52d8dd2768cb565352633 Mon Apr 24 15:21:37 2017 -0700
    Allow bigBarChart w/o offset/len into matrix. refs #18736
  • lines changed 2, context: html, text, full: html, text
    3baff3293826c9828f1a4f073edb910fe5afc9cc Mon Apr 24 15:33:39 2017 -0700
    Add default string for units, needed by R script args. refs #18736
  • lines changed 9, context: html, text, full: html, text
    c2aec133d337211ceb481cb51555d4af8bd29f97 Mon Apr 24 17:18:36 2017 -0700
    More robust. Handle missing trackDb settings, matrix columns, bed columns. refs #18736
  • lines changed 2, context: html, text, full: html, text
    570586117c6ddf545ab46a93775768d1ff04f89d Tue Apr 25 14:37:24 2017 -0700
    Clarify label as per QA request. refs #18736
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 12, context: html, text, full: html, text
    4c7c9dcefffa4971f5b666373e88cec3679301e9 Wed Apr 26 11:30:41 2017 -0700
    Try to accomodate big labels better -- adjust plot margins. refs #18736
  • lines changed 1, context: html, text, full: html, text
    ae9cca16d610361fb1ff65574d60ac709d1e84ec Wed Apr 26 12:47:21 2017 -0700
    Tweak threshold for larger plot margin. refs #18736
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 1, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 1, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 4, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 2, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 195, context: html, text, full: html, text
    7db53e413100cb37da4e8544b1683e20fa3faf72 Tue Apr 25 17:32:52 2017 -0700
    adding gene graph documentation, refs #13634
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 2, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 1, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 55, context: html, text, full: html, text
    88176813534c36dc29386c0d09f473b99b47fe50 Wed Apr 26 17:00:56 2017 -0700
    Adding settings doc for bigBarChart type track. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 55, context: html, text, full: html, text
    88176813534c36dc29386c0d09f473b99b47fe50 Wed Apr 26 17:00:56 2017 -0700
    Adding settings doc for bigBarChart type track. refs #18736
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 111, context: html, text, full: html, text
    88176813534c36dc29386c0d09f473b99b47fe50 Wed Apr 26 17:00:56 2017 -0700
    Adding settings doc for bigBarChart type track. refs #18736
• src/hg/htdocs/goldenPath/mapPlots/RHguide.html
  • lines changed 91, context: html, text, full: html, text
    919d1d090bc94536b383ca410bdea953ea7c30f3 Thu Apr 27 17:24:25 2017 -0700
    Removing obsolete mapPlots page, refs #17656
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    e718f1a1f7dfd09afd5baa80adba7d752afe41de Thu Apr 27 17:06:29 2017 -0700
    htdocs, cse-to-soe replacements, RM #19134
• src/hg/htdocs/training/index.html
  • lines changed 48, context: html, text, full: html, text
    add6faa96b0b8d5068cdde2cf5801a10f2e11c5d Fri Apr 28 11:49:20 2017 -0700
    dropping completed Howard, UVa, RNA-seq workshops. adding UPenn, JAX
• src/hg/inc/barChartBed.h
  • lines changed 1, context: html, text, full: html, text
    41d01fd0f045a58696edb753981feef6865f62e5 Mon Apr 24 15:11:24 2017 -0700
    1. Fix schema file syntax problem, strangely in comment. Caused crash in QA testing. 2. Allow bigBarChart w/o offset/len into matrix. refs #18736
• src/hg/inc/hdb.h
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    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/js/hgVarAnnogrator.js
  • lines changed 3, context: html, text, full: html, text
    d9c3524816e461a40daeb695088fd6e3d65aa379 Fri Apr 28 14:09:50 2017 -0700
    Don't show loadingImage when user is saving to a file because then it never goes away. refs #19305
• src/hg/lib/barChartBed.as
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    41d01fd0f045a58696edb753981feef6865f62e5 Mon Apr 24 15:11:24 2017 -0700
    1. Fix schema file syntax problem, strangely in comment. Caused crash in QA testing. 2. Allow bigBarChart w/o offset/len into matrix. refs #18736
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    2f4b2eb1df8521e7f931c3c8cb5d6d20e60384da Wed Apr 26 09:04:55 2017 -0700
    Updating the autoSql and sql files to include gene name, refs #19155
• src/hg/lib/barChartBed.sql
  • lines changed 1, context: html, text, full: html, text
    41d01fd0f045a58696edb753981feef6865f62e5 Mon Apr 24 15:11:24 2017 -0700
    1. Fix schema file syntax problem, strangely in comment. Caused crash in QA testing. 2. Allow bigBarChart w/o offset/len into matrix. refs #18736
  • lines changed 5, context: html, text, full: html, text
    2f4b2eb1df8521e7f931c3c8cb5d6d20e60384da Wed Apr 26 09:04:55 2017 -0700
    Updating the autoSql and sql files to include gene name, refs #19155
• src/hg/lib/customFactory.c
  • lines changed 13, context: html, text, full: html, text
    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    b8b17675d4f45ac91897edec324364415d38b64e Mon Apr 24 10:49:24 2017 -0700
    recognize $D in bigDataUrl's when checking to see if track data is available
  • lines changed 38, context: html, text, full: html, text
    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/lib/hgHgvs.c
  • lines changed 64, context: html, text, full: html, text
    b1291b0928de2ce364c5335642acfc457110641e Mon Apr 24 14:08:18 2017 -0700
    When an HGVS term maps to a base that has been deleted from the reference genome, e.g. NM_020469.2(ABO):c.261= maps to a deleted base in hg19 & hg38, pslTransMap returns NULL, so we were failing to map it to any genomic location. Added mapToDeletion for this special case, so we can map to the zero-length region where the reference genome has a deleted base.
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
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    70f54565f755ee8d55105606220d7ebaf04d2133 Mon Apr 24 14:41:54 2017 -0700
    Strange consequence of last commit for test case: ncbiRefSeqPsl has only one mapping to an _alt. refSeqAli has mappings to both chr11 and chr11_alt. Previously, pslMap would return NULL for the _alt mapping due to NM_000218.2:c.1071 being deleted in the _alt, and so we would fall back on refSeqAli and get its chr11 mapping. But now we are able to map to the location of the deletion, we get the _alt mapping but not the chr11 mapping because we no longer fall back on refSeqAli.
• src/hg/lib/wikiLink.c
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/hg/makeDb/doc/criGri1.txt
  • lines changed 92, context: html, text, full: html, text
    4c6ba35ce2bad0942aa551b280b72cb85e0b12d2 Tue Apr 25 10:15:00 2017 -0700
    lastz chainNet to criGriChoV1 refs #19228
• src/hg/makeDb/doc/criGriChoV1/initialBuild.txt
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    04e5a40b8a89cbb1293265dbb1a158e1f82f2cbc Tue Apr 25 13:38:32 2017 -0700
    run up lastz/chainNet to criGri1 for a track on the browser and finished into redmine release refs #19228
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
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    c8bc7a0411d5a630d45e39fdf4cd8e35edbc4ad9 Sun Apr 30 22:55:16 2017 -0700
    override ensGene link to pre.ensembl.org refs #19228
• src/hg/makeDb/trackDb/human/hg16/trackDb.chainNet.ra
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    6f6dee7c8c8580ffc3e6abc85a6179bea5251fe9 Thu Apr 27 13:08:04 2017 -0700
    Restoring phylo-order for the Comparative Genomics group for hg16, refs #19187
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
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    6f6dee7c8c8580ffc3e6abc85a6179bea5251fe9 Thu Apr 27 13:08:04 2017 -0700
    Restoring phylo-order for the Comparative Genomics group for hg16, refs #19187
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    f3e7d5374ba547373bc65ec648543d836e3841a1 Thu Apr 27 14:47:16 2017 -0700
    Restoring phylo-order for the Comparative Genomics group on hg17, refs #19187
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    f3e7d5374ba547373bc65ec648543d836e3841a1 Thu Apr 27 14:47:16 2017 -0700
    Restoring phylo-order for the Comparative Genomics group on hg17, refs #19187
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • lines changed 23, context: html, text, full: html, text
    f5b9063a4b598ec79f247182644b4424d3e8be98 Thu Apr 27 15:33:02 2017 -0700
    Restoring phylo-order for the Comparative Genomics group for hg18, refs #19187
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    f5b9063a4b598ec79f247182644b4424d3e8be98 Thu Apr 27 15:33:02 2017 -0700
    Restoring phylo-order for the Comparative Genomics group for hg18, refs #19187
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    85b7e127918eea3bcdbe83b6878fd7fcefedf76a Mon Apr 24 16:57:48 2017 -0700
    changing interactions track based on suggestions from Matt, refs #13634
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/hg/makeDb/trackDb/human/hg38/gtexTranscriptExpression.html
  • lines changed 133, context: html, text, full: html, text
    d2969146570b965afd380070ed85bf358201b3d6 Fri Apr 28 12:18:35 2017 -0700
    description page for the gtex transcript expression track, refs #19155
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    c2aec133d337211ceb481cb51555d4af8bd29f97 Mon Apr 24 17:18:36 2017 -0700
    More robust. Handle missing trackDb settings, matrix columns, bed columns. refs #18736
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    0c06510e49cf73b4dde95be6196567e51f1dd91a Tue Apr 25 14:34:24 2017 -0700
    Using bigBarChart as native track type. refs #18736
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/hg/makeDb/trackDb/human/snp147.shared.html
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    b8b2dce09e0073a4e609de53abb9aa2a8fffeb9f Tue Apr 25 11:03:46 2017 -0700
    Fixing minor typo, no RM
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    dc78a6c8eea53a9a40567f68badb9490a812297e Wed Apr 26 12:54:48 2017 -0700
    Editing Snp desc pgs to better describe weight field, refs #18330
• src/hg/makeDb/trackDb/human/snp149.shared.html
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    b8b2dce09e0073a4e609de53abb9aa2a8fffeb9f Tue Apr 25 11:03:46 2017 -0700
    Fixing minor typo, no RM
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    dc78a6c8eea53a9a40567f68badb9490a812297e Wed Apr 26 12:54:48 2017 -0700
    Editing Snp desc pgs to better describe weight field, refs #18330
• src/hg/makeDb/trackDb/human/trackDb.ra
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/hg/makeDb/trackDb/makefile
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    45d50037e7d7433f8197941c512e487567c17d63 Wed Apr 26 16:21:44 2017 -0700
    take criGriChoV1 off the list for a while refs #19228
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    731b5bfe0f7049622ab803a4f88bc0d65d594359 Thu Apr 27 14:31:02 2017 -0700
    removing some random gisaid thing I found, no redmine
• src/hg/makeDb/trackDb/tagTypes.tab
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    0c06510e49cf73b4dde95be6196567e51f1dd91a Tue Apr 25 14:34:24 2017 -0700
    Using bigBarChart as native track type. refs #18736
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    4339732995817c098782867b7c3f67d3af43204f Wed Apr 26 09:02:51 2017 -0700
    Adding bigBarChart to some of the accepted tag types, refs #19155
• src/hg/makeDb/trackDb/trackDb.transMap.ra
  • lines changed 5, context: html, text, full: html, text
    18e34853d35184f27c958d008ce5db5d97b85714 Wed Apr 19 12:46:27 2017 -0700
    Removing release tags for transMap V4 tracks ahead of public release, refs #18818
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    cee1dd7e5657e2156cc958d08ebe252444e02d45 Mon Apr 24 13:16:34 2017 -0700
    Adding Version 4 back to longLabels for transMap tracks, refs #18818 #19281
• src/hg/pyLib/hgLib.py
  • lines changed 512, context: html, text, full: html, text
    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/pyLib/makefile
  • lines changed 62, context: html, text, full: html, text
    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/pylib/hgLib.py
  • lines changed 508, context: html, text, full: html, text
    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
  • lines changed 508, context: html, text, full: html, text
    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/pylib/hgLib.pyo
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
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    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/pylib/makefile
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
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    2b9a3a726493d66c526e3d8256178ff3e12c7e3c Fri Apr 28 16:48:03 2017 -0700
    renaming pylib to pyLib after Angie's suggestion (thanks) and adding a better error message when graphviz was not found. refs #13634
• src/hg/regulate/regCluster/regCluster.c
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    1423088462963a58347aafb3bffe93b96a1665ed Thu Apr 27 12:30:43 2017 -0700
    Fix example in usage message. refs #19232
• src/hg/utils/markDownToHtml/markDownToHtml
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    db0b5db00903b7fb9513f88e785007252e0816ae Wed Apr 26 13:04:14 2017 -0700
    adding a quickly hacked converter for static pages used for gene interactions track doc page, refs #13634
• src/hg/utils/markDownToHtml/staticPage.html
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    db0b5db00903b7fb9513f88e785007252e0816ae Wed Apr 26 13:04:14 2017 -0700
    adding a quickly hacked converter for static pages used for gene interactions track doc page, refs #13634
• src/hg/utils/markDownToHtml/staticPage.lua
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    db0b5db00903b7fb9513f88e785007252e0816ae Wed Apr 26 13:04:14 2017 -0700
    adding a quickly hacked converter for static pages used for gene interactions track doc page, refs #13634
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
• src/inc/common.mk
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/inc/obscure.h
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    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
• src/inc/rSha1.h
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/inc/sha1.h
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    71b6403f90f9f221004a07cbd4e5aecedd9f6438 Mon Apr 24 12:41:27 2017 -0700
    Refs #17538. Adds ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an on-line server. It still supports the URL through UDC however, which is more efficient for large custom region lists and also provides backwards compatibility. Uses sha1 instead of md5 for faster speed now.
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
• src/index/makefile
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    fc3d3cbf826851710075abad58ed7277d0c250f7 Mon Apr 24 16:51:39 2017 -0700
    Cleaning up newlines in text strings and comments and adding to build.
• src/index/trixContextIndex/makefile
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    c240989c15afc0e39b1a3dc9158501759b3b31ba Mon Apr 24 16:49:25 2017 -0700
    A first cut at a utility that might be useful for returning context information on a trix search.
• src/index/trixContextIndex/trixContextIndex.c
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    c240989c15afc0e39b1a3dc9158501759b3b31ba Mon Apr 24 16:49:25 2017 -0700
    A first cut at a utility that might be useful for returning context information on a trix search.
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    fc3d3cbf826851710075abad58ed7277d0c250f7 Mon Apr 24 16:51:39 2017 -0700
    Cleaning up newlines in text strings and comments and adding to build.
• src/lib/hmac.c
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/https.c
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/makefile
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/obscure.c
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    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
• src/lib/rSha1.c
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/sha1.c
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    71b6403f90f9f221004a07cbd4e5aecedd9f6438 Mon Apr 24 12:41:27 2017 -0700
    Refs #17538. Adds ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an on-line server. It still supports the URL through UDC however, which is more efficient for large custom region lists and also provides backwards compatibility. Uses sha1 instead of md5 for faster speed now.
  • lines changed 240, context: html, text, full: html, text
    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
• src/lib/tests/makefile
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/tests/rSha1Test.c
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/lib/tests/sha1Test.c
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    71b6403f90f9f221004a07cbd4e5aecedd9f6438 Mon Apr 24 12:41:27 2017 -0700
    Refs #17538. Adds ability for user to paste a custom BED region into the multi-region dialog box instead of having to provide a URL to an on-line server. It still supports the URL through UDC however, which is more efficient for large custom region lists and also provides backwards compatibility. Uses sha1 instead of md5 for faster speed now.
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    5cc4a16511d6a2980e27a1225e2f90c72b5ea077 Wed Apr 26 14:19:28 2017 -0700
    -Renaming sha1 to rSha1 etc to avoid silent name collision during linking.
• src/lib/udc.c
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    4ddb5c55d4f4e8ad0375aab9bb2fad80d39b4c40 Mon Apr 24 16:34:06 2017 -0700
    refs #17358. Improves trash file touching for multi-region custom bed regions temp files.
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/product/README.building.source
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/product/installer/browserSetup.sh
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    9c36075677842f13a1655252218014bd0ddcf556 Wed Apr 26 09:59:51 2017 -0700
    gbic: fixing bug that appears with mariadb and a non-empty transaction log
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/userApps/Makefile
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/utils/bedBestTranscript
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    ae427c75bc1aa63033fb656a0f84ddc0c45486bf Fri Apr 28 18:03:13 2017 -0700
    Adding two more tools required for building the gene interactions track, refs #13634
• src/utils/bedJoinTabOffset
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    fb682f5daed16fba30b6f1b9d32cad52179113ed Mon Apr 24 16:55:59 2017 -0700
    bedJoinTabOffset: making sure that input file is tab-separated, refs #18736
• src/utils/bedNamePickFirst
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    ae427c75bc1aa63033fb656a0f84ddc0c45486bf Fri Apr 28 18:03:13 2017 -0700
    Adding two more tools required for building the gene interactions track, refs #13634
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    f9690acb15db4552ef45f4565e962acc8b3d5998 Wed Apr 26 09:05:43 2017 -0700
    Updating the expMatrixToBarchartBed script to include gene name in the final bed, refs #19155
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/expMatrixToBarchartBed/makefile
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/expMatrixToBarchartBed/tests/makefile
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/expMatrixToBarchartBed/tests/test.coords
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    f9690acb15db4552ef45f4565e962acc8b3d5998 Wed Apr 26 09:05:43 2017 -0700
    Updating the expMatrixToBarchartBed script to include gene name in the final bed, refs #19155
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/expMatrixToBarchartBed/tests/test.groupOrder
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/expMatrixToBarchartBed/tests/test.output
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    f9690acb15db4552ef45f4565e962acc8b3d5998 Wed Apr 26 09:05:43 2017 -0700
    Updating the expMatrixToBarchartBed script to include gene name in the final bed, refs #19155
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    a4586817cf3af50c1d03fe5886ae83b599e02575 Wed Apr 26 15:31:01 2017 -0700
    Broke the test data set for my python script, oops! refs #19155
• src/utils/expMatrixToBarchartBed/tests/test.output2
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    e00c621783b60bd6b781488b7e82f14b749ea92d Fri Apr 28 11:27:27 2017 -0700
    Fixing up the script and addressing the feedback from Kate, closes #19287
• src/utils/ggGeneClasses
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggGpmlToTag
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggKgmlToTab
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggMsrToTab
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggPidToTab
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggPpiToTab
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggSpfToTab
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/ggTables
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
• src/utils/makefile
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    6a71ffa8818ab34fd8bbbbc927e0f569c3c30386 Tue Apr 25 14:34:56 2017 -0700
    Fix whitespace.
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    16720e7dfab79a7f60e91f0cb102a213c3e4738a Fri Apr 28 15:39:08 2017 -0700
    first big commit for hgGeneGraph. Others will follow as QA progresses. refs #13634
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    ae427c75bc1aa63033fb656a0f84ddc0c45486bf Fri Apr 28 18:03:13 2017 -0700
    Adding two more tools required for building the gene interactions track, refs #13634
• src/utils/qa/bamToBedGraph.csh
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    597772d765cd83c500fb244b7ca513f8bed652f7 Tue Apr 25 07:56:26 2017 -0700
    added bedtools -split flag to ensure reads are not counted where they span an intron. improved sort so chromStart is properly sorted. Refs #19300
• src/utils/qa/weeklybld/buildEnv.csh
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    2d2d0d6547c581a258c8e21bc1dd7a1d32b1a36f Mon May 1 09:54:42 2017 -0700
    v349 preview1 refs #19231
• src/utils/qa/weeklybld/buildOneUseCase
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/utils/qa/weeklybld/buildWithUseCases
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/utils/qa/weeklybld/defaultBuildSettings.mk
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.
• src/utils/qa/weeklybld/downloadBuildSettings.mk
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    d9719e1d52b657fec9bf6676c85a4d2458fd7e89 Thu Apr 27 15:54:31 2017 -0700
    Remove optional compile switch USE_SSL so that openssl is now an official kent repo dependency. Also using openssl sha1 in hgTracks multiregion. refs #17358.

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