All File Changes

v350_base to v351_preview (2017-06-05 to 2017-06-12) v351

• src/browserbox/root/updateBrowser.sh
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    879760b7b88eacf89dab7012af3a9b030ba351b9 Fri Jun 9 12:22:23 2017 -0700
    updating the updateBrowser script in the tree, refs #19587
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    08dfa19bf3032887f066c3ab8943afef74fb8bee Fri Jun 9 14:50:41 2017 -0700
    fixing hg38 mysql update in gbib, refs #19587
• src/hca/README
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    7a07f877246c11849c7a6702688ca9513d4252be Fri Jun 2 14:27:40 2017 -0700
    Adding reference to LICENSE in README.
• src/hca/fromArrayExpress/README
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    f7d7de0807a969111b230bce983369e2bca2eba7 Sat Jun 3 13:25:02 2017 -0700
    Starting directory for importing projects from HCA.
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c
  • lines changed 153, context: html, text, full: html, text
    a55f333a7f05e2bcc03278b79eb13de371c275e5 Sun Jun 4 13:54:40 2017 -0700
    Start of reformatter from arrayExpress to HCA tagStorm. Wow, a lot of renaming and still not done with that, nevermind the more structural changes.
  • lines changed 6, context: html, text, full: html, text
    bbdcdd68f83d4f6ef38c7f1ba1e9a2a780cf1d29 Sun Jun 4 14:17:54 2017 -0700
    Have finished renaming and weeding pass for fields in our two examples at least. Still todo the reformatting.
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    e59125514ee9cfa47168f772f1f6dbea3fa5ac04 Sun Jun 4 20:28:55 2017 -0700
    Dealing with finding assay.seq.machine.
  • lines changed 127, context: html, text, full: html, text
    89ba7232309a06a09398d9207f71da284258ba66 Sun Jun 4 23:00:02 2017 -0700
    Dealing with idf.Person* tags. Also turning some weeding of redundant terms to more conservative 'replaceWithFirstChoice.
  • lines changed 39, context: html, text, full: html, text
    94f2c56cfbb4432f3152f3fc00b7c060e501e878 Sun Jun 4 23:20:15 2017 -0700
    Dealng with secondary accessions.
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    4d5d2ba756aab35dd74626d7514a8c77fdc319b6 Mon Jun 5 00:03:51 2017 -0700
    Coping with DDJB trace accessions and combining text and data supplementary files into a single array.
  • lines changed 68, context: html, text, full: html, text
    ed1a3ec8c86add73020e7592b4cd8675b962868e Mon Jun 5 07:50:03 2017 -0700
    Dealing with seq.paired_ends, rna.strand, and improving seq.molecule.
  • lines changed 115, context: html, text, full: html, text
    a905cf6faa256af0adad4809d68b6ef2c5639314 Thu Jun 8 21:59:00 2017 -0700
    Handling protocols.
  • lines changed 52, context: html, text, full: html, text
    255671c6b58617b6309ab4d1a2ccf09edca53e74 Fri Jun 9 14:30:53 2017 -0700
    Lots of little fixes to vocabulary. Adding donor.uuid.
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    a55f333a7f05e2bcc03278b79eb13de371c275e5 Sun Jun 4 13:54:40 2017 -0700
    Start of reformatter from arrayExpress to HCA tagStorm. Wow, a lot of renaming and still not done with that, nevermind the more structural changes.
  • lines changed 1, context: html, text, full: html, text
    d4227924efd51f8fd1f88b373653cbc475e06ec3 Fri Jun 9 20:14:30 2017 -0700
    Linking with uuid library.
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/test.tags
  • lines changed 192, context: html, text, full: html, text
    a55f333a7f05e2bcc03278b79eb13de371c275e5 Sun Jun 4 13:54:40 2017 -0700
    Start of reformatter from arrayExpress to HCA tagStorm. Wow, a lot of renaming and still not done with that, nevermind the more structural changes.
  • lines changed 1, context: html, text, full: html, text
    3ffa8a1e5efde2b3e3600249290f0d8293a6d035 Thu Jun 8 23:15:20 2017 -0700
    Adding a line accidentally deleted back into test set.
• src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c
  • lines changed 150, context: html, text, full: html, text
    831bc70506c43ba97b550c4f8d001f130eef97a0 Sat Jun 3 16:02:05 2017 -0700
    Utility to convert ArrayExpress tab-sep-files to a tagStorm is fully half baked now. Handling first of two tab-sep-files.
  • lines changed 93, context: html, text, full: html, text
    44f45592a7dacc9006180ccc5df5267467c15bb9 Sat Jun 3 17:35:43 2017 -0700
    First cut of parsing sdrf.txt file. Still got to deal better with term-source-refs and term-accessions.
  • lines changed 15, context: html, text, full: html, text
    5f85700e04280b91f910b5b76ac2a06dff1d1f14 Sat Jun 3 18:20:47 2017 -0700
    Dealing with Term Source REF and Term Accession Number's dependency on previous fields.
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    4fb316961e495d2667b021a8f8eb1e6b57f7522f Sat Jun 3 18:31:29 2017 -0700
    Dealing with repeated SecondaryAccession in idf files.
  • lines changed 2, context: html, text, full: html, text
    f19c68a052a2712449f2bf6ce72f3d9c37f7785d Sat Jun 3 18:41:13 2017 -0700
    Relaxing some error checking that was causing problems, skip instead of errAbort.
  • lines changed 9, context: html, text, full: html, text
    0a292e50dbc126ea297f1305b909920ced7765b0 Sun Jun 4 14:18:58 2017 -0700
    Handling Unit, which like the ontology term stuff, occurs anywhere and modifies previous fields.
  • lines changed 11, context: html, text, full: html, text
    8b00e74bab400cad7e2a56d57f268281ea9c56ca Thu Jun 8 23:17:01 2017 -0700
    Removing trailing underbar from array express field names. Removing required fields in sdrf since they vary so much between submissions.
  • lines changed 1, context: html, text, full: html, text
    05aac510eef09c3873d1885b49a660259c19fb92 Fri Jun 9 20:14:57 2017 -0700
    Fixing reversal of stanzas.
• src/hca/fromArrayExpress/arrayExpressToTagStorm/makefile
  • lines changed 3, context: html, text, full: html, text
    11f4fabd36716bcce6cc27b91464b27e48cd7682 Sat Jun 3 16:02:11 2017 -0700
    Utility to convert ArrayExpress tab-sep-files to a tagStorm is fully half baked now. Handling first of two tab-sep-files.
• src/hca/fromArrayExpress/arrayExpressToTagStorm/test.idf.txt
  • lines changed 32, context: html, text, full: html, text
    fe441da309997cb46221c512dc7d7c32a99b998a Sat Jun 3 13:31:06 2017 -0700
    Adding test set for arrayExpressToTagStorm program.
  • lines changed 1, context: html, text, full: html, text
    f8b86d1a5a8ad658ce2179cfd9011d841af2adfd Thu Jun 8 23:17:40 2017 -0700
    Adding a line accidentally deleted back into test set.
• src/hca/fromArrayExpress/arrayExpressToTagStorm/test.sdrf.txt
  • lines changed 7, context: html, text, full: html, text
    fe441da309997cb46221c512dc7d7c32a99b998a Sat Jun 3 13:31:06 2017 -0700
    Adding test set for arrayExpressToTagStorm program.
• src/hca/fromGeo/README
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoSoftToRaDir/geoSoftToRaDir.c
  • lines changed 154, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
  • lines changed 154, context: html, text, full: html, text
    937dc7a7db8bb221cb28cf32ce99e05a19a92205 Fri Jun 2 14:30:08 2017 -0700
    Moving not so useful utility that has been superceded by geoToTagStorm to place where it doesn't need code review.
• src/hca/fromGeo/geoSoftToRaDir/makefile
  • lines changed 3, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
  • lines changed 3, context: html, text, full: html, text
    937dc7a7db8bb221cb28cf32ce99e05a19a92205 Fri Jun 2 14:30:08 2017 -0700
    Moving not so useful utility that has been superceded by geoToTagStorm to place where it doesn't need code review.
• src/hca/fromGeo/geoStormToHcaStorm/expected.tags
  • lines changed 204, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
  • lines changed 224, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    cbb6973cb9210c1b1395a638210a734794d0c920 Fri Jun 2 14:27:01 2017 -0700
    Leaving supplementary files in
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    79eecd27f9665f13b7fb3658f19b2e25727974b8 Sat Jun 3 19:09:58 2017 -0700
    Changing date format to YYYY-MM-YY.
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    58fcdf39c0eb2d0d7418116727e30cc904398a0b Tue Jun 6 17:16:04 2017 -0700
    Handling sample.donor.age, sample.donor.body_mass_index, sample.donor.age. Also swapping . for _ in contact.
  • lines changed 72, context: html, text, full: html, text
    98d5d71a7d203bcdb4779b73645f9465d1e20ce9 Thu Jun 8 23:21:03 2017 -0700
    Quite a few small changes. Adding project uuid. Making a combined address tag to be more euro-friendly. Refactoring tag storm tree traversal code so don't need 6 lines to wrap every routine that traverses the tree.
  • lines changed 56, context: html, text, full: html, text
    6a7f1c0079c6959aad2c38688c56f64bf3f71016 Fri Jun 9 00:10:34 2017 -0700
    Improving commening and making protocols go into an array.
  • lines changed 13, context: html, text, full: html, text
    0090d76d39cafaa67b70ae78ade2cccdd3ea88b4 Fri Jun 9 20:15:29 2017 -0700
    Adding makeUuidString to library.
• src/hca/fromGeo/geoStormToHcaStorm/in.tags
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoStormToHcaStorm/makefile
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    98d5d71a7d203bcdb4779b73645f9465d1e20ce9 Thu Jun 8 23:21:03 2017 -0700
    Quite a few small changes. Adding project uuid. Making a combined address tag to be more euro-friendly. Refactoring tag storm tree traversal code so don't need 6 lines to wrap every routine that traverses the tree.
• src/hca/fromGeo/geoStormToHcaStorm/srxToSrr.tab
  • lines changed 48, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoToTagStorm/expected.tags
  • lines changed 249, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoToTagStorm/geoToHca.delete
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    d0d7db3bc684ca5e714ddcab080de393f24d2687 Fri Jun 2 14:26:19 2017 -0700
    Some external files have been integrate into C code of geoStormToHcaStorm.
• src/hca/fromGeo/geoToTagStorm/geoToHca.rename
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    d0d7db3bc684ca5e714ddcab080de393f24d2687 Fri Jun 2 14:26:19 2017 -0700
    Some external files have been integrate into C code of geoStormToHcaStorm.
• src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c
  • lines changed 346, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    fef6b0e6ceee0f85c4a88300de55419d379901a5 Thu Jun 8 23:22:46 2017 -0700
    Adding plural to some tag names made from arrays. Keeping program from reversing order of things.
• src/hca/fromGeo/geoToTagStorm/makefile
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/geoToTagStorm/test.soft
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/hcaAddSrrFiles/expected.tags
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
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    7380cf43b63d424791325dba3711392044723fea Fri Jun 2 14:28:23 2017 -0700
    Removing some debugging statements and fixing Offset/Size mixup.
• src/hca/fromGeo/hcaAddSrrFiles/makefile
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/fromGeo/hcaAddSrrFiles/test.tags
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/oneShot/geoSoftToRaDir/geoSoftToRaDir.c
  • lines changed 154, context: html, text, full: html, text
    937dc7a7db8bb221cb28cf32ce99e05a19a92205 Fri Jun 2 14:30:08 2017 -0700
    Moving not so useful utility that has been superceded by geoToTagStorm to place where it doesn't need code review.
• src/hca/oneShot/geoSoftToRaDir/makefile
  • lines changed 3, context: html, text, full: html, text
    937dc7a7db8bb221cb28cf32ce99e05a19a92205 Fri Jun 2 14:30:08 2017 -0700
    Moving not so useful utility that has been superceded by geoToTagStorm to place where it doesn't need code review.
• src/hca/oneShot/hcaTsvToJson2/hcaTsvToJson2.c
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    ffa70570b6ea9aa319297d1fc83cd7f6f3aee7ba Fri Jun 9 20:16:08 2017 -0700
    Moving makeUuidString to library.
• src/hca/reformat/geoSoftToRaDir/geoSoftToRaDir.c
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoSoftToRaDir/makefile
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoStormToHcaStorm/expected.tags
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    2c7a7278b17c56cf7bb58e939a6f149530471c04 Thu Jun 1 21:54:02 2017 -0700
    Oops, meant to add expected.tags, not out.tags
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoStormToHcaStorm/geoStormToHcaStorm.c
  • lines changed 199, context: html, text, full: html, text
    373475aaf70e6b0eb02c5464fe9110f25fe9f24c Thu Jun 1 17:55:34 2017 -0700
    Utility to HCAify a GEO tagStorm. Will still need SRA files attached.
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    53af5fcd9de6582a30f2ab0405fb0c703fa38b91 Thu Jun 1 21:56:46 2017 -0700
    Adding srxToSrr.tab parameter and associated assay.sra_run tag. Renaming a few other tags in the output.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoStormToHcaStorm/in.tags
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    373475aaf70e6b0eb02c5464fe9110f25fe9f24c Thu Jun 1 17:55:34 2017 -0700
    Utility to HCAify a GEO tagStorm. Will still need SRA files attached.
  • lines changed 249, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoStormToHcaStorm/makefile
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    373475aaf70e6b0eb02c5464fe9110f25fe9f24c Thu Jun 1 17:55:34 2017 -0700
    Utility to HCAify a GEO tagStorm. Will still need SRA files attached.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoStormToHcaStorm/out.tags
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    7fb5e1977f5ea547629e349327664dc83db47b4a Thu Jun 1 21:52:59 2017 -0700
    Adding a test set.
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    2c7a7278b17c56cf7bb58e939a6f149530471c04 Thu Jun 1 21:54:02 2017 -0700
    Oops, meant to add expected.tags, not out.tags
• src/hca/reformat/geoStormToHcaStorm/srxToSrr.tab
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    7fb5e1977f5ea547629e349327664dc83db47b4a Thu Jun 1 21:52:59 2017 -0700
    Adding a test set.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/expected.tags
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    4b9efdf7b6d90698e486d8f1ccdd3132456ddc1b Thu Jun 1 17:11:31 2017 -0700
    Adding a test set.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/geoToHca.delete
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/geoToHca.rename
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/geoToTagStorm.c
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    ec6b7d8016ad341a64aacc6e7680214da34b6299 Thu Jun 1 12:17:14 2017 -0700
    Removing renaming and deleting bits. This will happen in another program specific to HCA. Skipping DATABASE level as it is always the same. Turning _1 _2 _3 etc into array.
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    20918bcae46467138245dd98cf4f2567e4fa18b8 Thu Jun 1 16:57:11 2017 -0700
    Making it by default collapse multiple tags with the same name in a stanza into a single comma-separated-list valued tag. The old behavior, which is occassionally useful, is avilable with the new expandArrays option.
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    4c2ca21cf82719c27ab53d4b1a00d8e90702747a Thu Jun 1 16:59:20 2017 -0700
    Oops forgot to add expandArrays to options[] table. Also downgrading some verbosities.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/makefile
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/geoToTagStorm/test.soft
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    4b9efdf7b6d90698e486d8f1ccdd3132456ddc1b Thu Jun 1 17:11:31 2017 -0700
    Adding a test set.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/hcaAddSrrFiles/expected.tags
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    76afc28e12ab0a404ba8f6668c8f02e4d53ee5a9 Thu Jun 1 23:07:57 2017 -0700
    Program to add several tags including the assay.files tag based on the sra_run and the paired_ends and single_cell.method tags.
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    3b03dacd234f1eb006be4ac3aade74f2c1b4cd24 Thu Jun 1 23:11:53 2017 -0700
    Oops, _1 _2, not _0 _1 in paired ends.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/hcaAddSrrFiles/hcaAddSrrFiles.c
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    76afc28e12ab0a404ba8f6668c8f02e4d53ee5a9 Thu Jun 1 23:07:57 2017 -0700
    Program to add several tags including the assay.files tag based on the sra_run and the paired_ends and single_cell.method tags.
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    3b03dacd234f1eb006be4ac3aade74f2c1b4cd24 Thu Jun 1 23:11:53 2017 -0700
    Oops, _1 _2, not _0 _1 in paired ends.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/hcaAddSrrFiles/makefile
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    76afc28e12ab0a404ba8f6668c8f02e4d53ee5a9 Thu Jun 1 23:07:57 2017 -0700
    Program to add several tags including the assay.files tag based on the sra_run and the paired_ends and single_cell.method tags.
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    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/reformat/hcaAddSrrFiles/test.tags
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    76afc28e12ab0a404ba8f6668c8f02e4d53ee5a9 Thu Jun 1 23:07:57 2017 -0700
    Program to add several tags including the assay.files tag based on the sra_run and the paired_ends and single_cell.method tags.
  • lines changed 207, context: html, text, full: html, text
    f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700
    Renaming directory to something more specific.
• src/hca/toHca/README
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    4e3095bc06307daed680b0300031c9b8ec26c6ba Fri Jun 2 08:33:29 2017 -0700
    Making directory for programs that assist in conversion to HCA submission formats.
• src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c
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    0b9219668c0793d20092ecd6128df8cf41025900 Fri Jun 2 14:16:34 2017 -0700
    First cut works. Need to add some special casing for the files[] still.
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    fd67631b1660daf25b69d5a2df7643c4c75568b6 Fri Jun 2 14:23:31 2017 -0700
    Replacing local escaper with one from json library.
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    f29661c17a6bdc41aaa7cd7d4e8599be0910246b Fri Jun 2 14:35:05 2017 -0700
    Moving tagStormListLeaves to library.
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    80391fd4f66e266ae5ac2b0bddcffbce9c5390e8 Fri Jun 2 14:39:06 2017 -0700
    Moving pathsInDirAndSubdirs to library.
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    53b998b52efc314f64d9d03bc6e3cb49269a38c3 Thu Jun 8 23:26:06 2017 -0700
    Much more complete implementation. Will create json arrays[] automatically if it's a tagStorm array better. Makes type field semi credibly inside of files object array.
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    1873efca603354ee97fddf8947f564244fc65a2b Fri Jun 9 20:18:36 2017 -0700
    Fixing double write of files array. Treating urls as a special directory where the data just lives somewhere on the web.
• src/hca/toHca/hcaStormToBundles/test.tags
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
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    9f9ad5fdcccb6e5f697a016d2957bbe4757f7e87 Thu Jun 8 23:27:02 2017 -0700
    Changing to index1_reads2 instead of index1_data2 as paired_ends description for 10x-v2 and drop-seq.
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    4da8f87d4bff04bfcc27509e10ac97739a32b46c Fri Jun 9 20:16:59 2017 -0700
    Moving protocols to an array.
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587500_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587501_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587502_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587503_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587504_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587505_1.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587500_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587501_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587502_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587503_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587504_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587505_2.fastq.gz
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    a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700
    Making a test set for hcaStormToBundles
• src/hca/toHca/hcaStormToBundles/testIt
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    0b9219668c0793d20092ecd6128df8cf41025900 Fri Jun 2 14:16:34 2017 -0700
    First cut works. Need to add some special casing for the files[] still.
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    05686549b44546d1095e575291d5356007408e51 Fri Jun 9 20:17:34 2017 -0700
    Printing out an assay.json after test.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
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    0a7a102e1881380993522ec0204c5f9e12c7257c Mon Jun 5 16:52:24 2017 -0700
    adding .tsv support to cdwMakeValidFile
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
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    0cc76b8a1e9ab5b02f12e7463893dc324760e838 Thu Jun 8 20:53:26 2017 -0700
    cdwWebBrowse: Adding navigation first prev next last links. Also made it reset the page number back to 1 if anything changed such as: clear search button pressed, search changed, filters changed. FYI sort-change already took care of resetting the page number.
• src/hg/hgComposite/hgComposite.c
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    3ec039397b40eaa784d02994512b9bc5d69ae1c8 Sun Jun 11 15:50:34 2017 -0700
    ongoing work on hgComposite
• src/hg/hgGeneGraph/hgGeneGraph
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    0aa638ae2c6f3d2ee4e1b06ad91166c5eaef58cc Tue Jun 6 13:19:55 2017 -0700
    adding a line break for large screens, refs #13634
• src/hg/hgGeneGraph/makefile
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    4e58f720cc61c696f740527a5a8282a2e4582df0 Tue Jun 6 10:31:21 2017 -0700
    correct remove targets refs #19559
• src/hg/hgMirror/hgMirror
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    13ce609f4d51ff95a108be6224d92aab0a8660a2 Fri Jun 9 12:17:27 2017 -0700
    addessing hgdownload slowness and hg38 in hgMirror, refs #19587
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    5cbddfd6de0659a4143ccd85fb58272ad9e1a37e Fri Jun 9 15:33:40 2017 -0700
    fixing bug in hgMirror, thanks ChrisL, refs #19587
• src/hg/htdocs/FAQ/FAQreleases.html
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    8d7bb0007f2ccf8a718a485c1bdf8c3a3fcb3a07 Tue Jun 6 09:59:53 2017 -0700
    editing html pages per refs #16628
• src/hg/htdocs/FAQ/FAQtracks.html
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    8dc0cda1053485e5cbaae2b623c8a3a3d4365441 Mon Jun 5 13:44:10 2017 -0700
    Minor edits from code review, refs #19545
• src/hg/htdocs/goldenPath/credits.html
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    8d7bb0007f2ccf8a718a485c1bdf8c3a3fcb3a07 Tue Jun 6 09:59:53 2017 -0700
    editing html pages per refs #16628
• src/hg/htdocs/goldenPath/help/barChart.html
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    f9bcc991f561fed7bf96e4ed282f6bd64f28a6a3 Tue Jun 6 14:09:14 2017 -0700
    Fixing broken link as per code review, refs #19543
• src/hg/htdocs/goldenPath/help/gbic.html
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
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    b338966668dd97a8721e0cb5ec09f1d21b532a91 Tue Jun 6 11:53:19 2017 -0700
    fixing links to archived versions of external stale databases on geneGraph page, refs #13634
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    520f159d64f8211d6b2ae7f1c3658a816550b563 Thu Jun 8 11:09:20 2017 -0700
    Adding notes about URL parameters on Track Hubs Doc page refs #19578
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    205aa46c50c19f6cc8e2096a149e0c53e572a688 Thu Jun 8 13:08:33 2017 -0700
    Adding some hints about sessions in the track hub user guide per input refs #19578
• src/hg/htdocs/goldenPath/help/mirror.html
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    fcc4fe0c52160f8b96453c180247a527fdc8f26e Mon Jun 5 13:29:30 2017 -0700
    making the mirror instructions a bit clearer, no redmine yet
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    f519936c321a3b8c80b806f9b1d4b07624991e66 Mon Jun 5 15:39:38 2017 -0700
    updating mirror manual to make it easier to read. no redmine yet
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/hg/htdocs/goldenPath/newsarch.html
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    ca714c8d25cbb1ca947983658a86b45217e4fbdc Tue Jun 6 08:35:39 2017 -0700
    editing newarch.html for ciona per refs #16628
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    305e27f0df71f358ecda43b21d4914967ab4850b Thu Jun 8 09:19:31 2017 -0700
    Adding vai.pl announcement, refs #12216
• src/hg/htdocs/images/oviAri3.jpg
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    db2e8920760e7c9741262b9e6b29a214e0390d80 Thu Jun 8 10:25:33 2017 -0700
    photo courtesy Malin P. Tygesen and Jacob B. Hansen, Univ. Copenhagen, Denmark - http://www1.bio.ku.dk/cbp/metabolic_regulation_lab/ refs #19237
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    efaa02d2b04c51116754098efa34fc0eae69a69b Thu Jun 8 10:38:08 2017 -0700
    correctly crop out white space at the bottom refs #19237
• src/hg/htdocs/inc/globalNavBar.inc
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    4003fa8463e0442d80728b55245f741ca55495a7 Tue Jun 6 11:46:30 2017 -0700
    changing position of interaction viewer in the menu after feedback from matt, refs #13634
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    0d820d31a2cf8820aa6b18e1feb8770b098c3a0d Fri Jun 9 16:12:52 2017 -0700
    commenting out gene graph as per Matt
• src/hg/htdocs/indexNews.html
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    3f8622ee9acf8a1f18a6b7c09ea5c657cad21b65 Tue Jun 6 09:18:59 2017 -0700
    edited indexNews for ciona release per refs #16628
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    8d7bb0007f2ccf8a718a485c1bdf8c3a3fcb3a07 Tue Jun 6 09:59:53 2017 -0700
    editing html pages per refs #16628
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    bef0f1bf62d6c705787c14fab600ab04ae84019e Tue Jun 6 10:04:23 2017 -0700
    edited indexNews per refs #16628
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    305e27f0df71f358ecda43b21d4914967ab4850b Thu Jun 8 09:19:31 2017 -0700
    Adding vai.pl announcement, refs #12216
• src/hg/lib/hgHgvs.c
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    029e75e2b3558b8c136e8ea4761bf181747627ac Wed Jun 7 11:43:56 2017 -0700
    Doh, HGVS n. search was not supported for NR_ terms with which it is usually used. refs #19423 note-3
• src/hg/lib/mathWig.c
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    3ec039397b40eaa784d02994512b9bc5d69ae1c8 Sun Jun 11 15:50:34 2017 -0700
    ongoing work on hgComposite
• src/hg/lib/tablesTables.c
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    e9203da9b6c1b668e21f5624768b4d7cc5c725d0 Wed Jun 7 13:25:21 2017 -0700
    CIRM: convert reset all to a button, as per Jim
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    0cc76b8a1e9ab5b02f12e7463893dc324760e838 Thu Jun 8 20:53:26 2017 -0700
    cdwWebBrowse: Adding navigation first prev next last links. Also made it reset the page number back to 1 if anything changed such as: clear search button pressed, search changed, filters changed. FYI sort-change already took care of resetting the page number.
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    974cc2a7d3e09e51252b36281d7e17a3897fdf18 Thu Jun 8 21:02:28 2017 -0700
    resolved merge conflict
• src/hg/makeDb/doc/danRer11/initialBuild.txt
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    e9e45576e42c6c2241551530542dd462308e1e19 Wed Jun 7 13:50:45 2017 -0700
    Adding initialBuild for the danRer11, refs #19459
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    6df0ad73366b7a61d5cb324370f0d41f838d487f Wed Jun 7 16:07:44 2017 -0700
    INSDC naming, refs #19459
• src/hg/makeDb/doc/equCab2.txt
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    af45f88e0df3c783edb5ae37fb53a0baf54bc315 Mon Jun 5 10:31:41 2017 -0700
    adding hg38 chainNet procedure refs #19511
• src/hg/makeDb/doc/hg38/quakeExpr.txt
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    a63c01d2e36d95854b442f26ba1b57e7f8262e3a Tue Jun 6 16:56:17 2017 -0700
    Adding trackDb changes, html files and documentation for new Quake expression track, refs #19517
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.augustus.html
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    c81023ffa6402ccb7542f1250d0fc608961bdea4 Thu Jun 8 09:56:36 2017 -0700
    fixup gene count and bases covered measurements refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/html/GCA_001624505.1_DBA_2J_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/html/GCA_001624535.1_FVB_NJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/html/GCA_001624675.1_NOD_ShiLtJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/html/GCA_001624745.1_NZO_HlLtJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/html/GCA_001624775.1_PWK_PhJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/html/GCA_001624835.1_WSB_EiJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/html/GCA_001624865.1_SPRET_EiJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/html/GCA_001632525.1_BALB_cJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/html/GCA_001632555.1_C57BL_6NJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/html/GCA_001632575.1_C3H_HeJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/html/GCA_001632615.1_LP_J_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.description.html
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    9a1d30729ffcacd5d9ca974e684c14577d357b3b Wed Jun 7 10:30:11 2017 -0700
    fixup assembly FTP links to NCBI refs #13553
• src/hg/makeDb/genbank/etc/genbank.conf
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    8389fcbe5331ee5c02257048f69bb9f59159ce79 Wed Jun 7 13:44:19 2017 -0700
    Added danRer11; refs #19459
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
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    4302440a883c4d3ec1277ea0007bf3bf271b3e57 Sun Jun 11 16:01:23 2017 -0700
    output an extended genePred
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.chainNet.ra
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    278b0f6daad0f41fd882b4108b09526060eda2b6 Fri Jun 9 12:57:12 2017 -0700
    Adding overrides for human chain/net tracks on equCab2 so that both hg19 and hg38 can coexist, no redmine
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
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    a63c01d2e36d95854b442f26ba1b57e7f8262e3a Tue Jun 6 16:56:17 2017 -0700
    Adding trackDb changes, html files and documentation for new Quake expression track, refs #19517
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
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    e298a94391ab589b304fe9dd4e2b67dafcc5612b Tue Jun 6 10:33:25 2017 -0700
    Changing track names to fix some bugs spotted by Chris Lee, refs #19154
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    b245e6345d72319b0cc1167ec7446401dfe80e8e Thu Jun 8 10:34:49 2017 -0700
    Fixing bigDataUrl lines in mappability track, refs #19154
• src/hg/makeDb/trackDb/human/hg38/quakeExpr.html
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    a63c01d2e36d95854b442f26ba1b57e7f8262e3a Tue Jun 6 16:56:17 2017 -0700
    Adding trackDb changes, html files and documentation for new Quake expression track, refs #19517
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    8a893c3abae0f55ac536030437ad11969254b0df Mon Jun 5 11:06:25 2017 -0700
    Adding the maxWindowToDraw trackDb setting to the Mouse SNPs track on mm10, refs #18305
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    36a6b2125663cc013db12c0a2afaf8a517d4b507 Mon Jun 5 13:54:53 2017 -0700
    Adding alpha and beta release tags to the strainSNPs track on mm10, refs #18305
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    7abdfab880e1e8373a645ae1c9353dd125160a6e Tue Jun 6 09:34:14 2017 -0700
    Change default vis from pack to dense per Jim's request, no redmine
• src/hg/makeDb/trackDb/sheep/oviAri3/description.html
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    c25b0a10b47fd3798f39dfffb36d5d428503439a Thu Jun 8 10:40:14 2017 -0700
    updated photograph from Malin P. Tygesen and Jacob B. Hansen refs #19237
• src/hg/makeDb/trackDb/trackDb.chainNet.other.ra
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    142f362b92f1743eb7d8fcbb4e585d7ccedda1ba Mon Jun 5 10:55:51 2017 -0700
    removing release tag alpha and beta to make ci3 public per refs #16628
• src/hg/makefile
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    6d5620611393538b633060375010ff15c476ace1 Mon Jun 5 15:26:08 2017 -0700
    Adding hgGeneGraph to src/hg/makefile
• src/hg/oneShot/freen/freen.c
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    b168eec18c0cb3f2d06b1ccc59eb34776403f50e Wed May 31 18:05:09 2017 -0700
    Writing and testing new csvParseNext function.
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    15f70a1451e9791fc080647cb8d913a5a6e0aa3b Wed May 31 18:17:40 2017 -0700
    Adding csvNeedsParsing
• src/hg/pyLib/makefile
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    fdd2ecea68d75d0a52d365473c1df7416f3e7f75 Mon Jun 5 10:58:42 2017 -0700
    fixup beta build refs #19473
• src/hg/utils/makefile
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    3befa37afeed7e94561d5d38cd429744ffe377f3 Tue Jun 6 09:56:58 2017 -0700
    scripts need to go out with make utils no redmine
• src/hg/utils/trashLoad/trashLoad.c
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    ad0f19ab3b6f5d24bade3c1a4f13825351c5a518 Tue Jun 6 09:28:26 2017 -0700
    checking for error on write to detect difficulties for trash Apocalypse testing no redmine
• src/hg/utils/trashRead/makefile
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    03df8df08572351d84eb9a23359be3706efa7ee0 Tue Jun 6 09:27:36 2017 -0700
    adding reading test for the trash Apocalypse testing no redmine
• src/hg/utils/trashRead/trashRead.c
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    03df8df08572351d84eb9a23359be3706efa7ee0 Tue Jun 6 09:27:36 2017 -0700
    adding reading test for the trash Apocalypse testing no redmine
• src/inc/common.h
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    e1a3e66b150100bcb49a4d995aeb38ff95fe43d2 Thu Jun 8 23:28:29 2017 -0700
    Made nextStringBetween for when you are looking repeatedly for a pattern.
• src/inc/csv.h
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    b168eec18c0cb3f2d06b1ccc59eb34776403f50e Wed May 31 18:05:09 2017 -0700
    Writing and testing new csvParseNext function.
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    15f70a1451e9791fc080647cb8d913a5a6e0aa3b Wed May 31 18:17:40 2017 -0700
    Adding csvNeedsParsing
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    2e2fe42ea116b0a37fe3bd4b1744a0998a4ccaa6 Fri Jun 2 14:24:09 2017 -0700
    Adding csvParse.
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    735cf928eb52e73b26027b1c9800a8922b3eb078 Sat Jun 3 17:07:49 2017 -0700
    Adding csvEscapeAndAppend
• src/inc/hash.h
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    32a7f051b082da240f3bc95d5419687a2d1fff93 Thu Jun 1 21:51:52 2017 -0700
    Adding hashReverseAllBucketLists, refactored out of hashExpand().
• src/inc/portable.h
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    80391fd4f66e266ae5ac2b0bddcffbce9c5390e8 Fri Jun 2 14:39:06 2017 -0700
    Moving pathsInDirAndSubdirs to library.
• src/inc/tagStorm.h
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    29fba277b1b4bc7e4d9ee3897b9e97fb73e30db7 Fri Jun 2 14:24:29 2017 -0700
    Fixing comment.
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    f29661c17a6bdc41aaa7cd7d4e8599be0910246b Fri Jun 2 14:35:05 2017 -0700
    Moving tagStormListLeaves to library.
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    045ffea66c916d05cb813b6751e3513ce979795d Sun Jun 4 12:09:56 2017 -0700
    Refactoring tagStormToTab to optionally handle csv output for cirm.
• src/inc/uuid.h
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    ce3b570cf3c96344383503946cd71e05a2e29870 Fri Jun 9 11:57:35 2017 -0700
    Starting a local uuid module with makeUuidString.
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    92fa558a39565702960b8ff54d3d9b0250e05410 Fri Jun 9 20:13:45 2017 -0700
    Adding constant for UUID_STRING_SIZE
• src/lib/common.c
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    e1a3e66b150100bcb49a4d995aeb38ff95fe43d2 Thu Jun 8 23:28:29 2017 -0700
    Made nextStringBetween for when you are looking repeatedly for a pattern.
• src/lib/csv.c
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    b168eec18c0cb3f2d06b1ccc59eb34776403f50e Wed May 31 18:05:09 2017 -0700
    Writing and testing new csvParseNext function.
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    15f70a1451e9791fc080647cb8d913a5a6e0aa3b Wed May 31 18:17:40 2017 -0700
    Adding csvNeedsParsing
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    2e2fe42ea116b0a37fe3bd4b1744a0998a4ccaa6 Fri Jun 2 14:24:09 2017 -0700
    Adding csvParse.
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    735cf928eb52e73b26027b1c9800a8922b3eb078 Sat Jun 3 17:07:49 2017 -0700
    Adding csvEscapeAndAppend
• src/lib/hash.c
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    32a7f051b082da240f3bc95d5419687a2d1fff93 Thu Jun 1 21:51:52 2017 -0700
    Adding hashReverseAllBucketLists, refactored out of hashExpand().
• src/lib/makefile
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    ce3b570cf3c96344383503946cd71e05a2e29870 Fri Jun 9 11:57:35 2017 -0700
    Starting a local uuid module with makeUuidString.
• src/lib/portimpl.c
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    80391fd4f66e266ae5ac2b0bddcffbce9c5390e8 Fri Jun 2 14:39:06 2017 -0700
    Moving pathsInDirAndSubdirs to library.
• src/lib/rqlParse.c
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    16313e67e6b0d8ab72b914a352a8cca2d81c4fa1 Thu Jun 8 23:28:49 2017 -0700
    Allowing '.' in a field name.
• src/lib/tagStorm.c
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    f29661c17a6bdc41aaa7cd7d4e8599be0910246b Fri Jun 2 14:35:05 2017 -0700
    Moving tagStormListLeaves to library.
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    045ffea66c916d05cb813b6751e3513ce979795d Sun Jun 4 12:09:56 2017 -0700
    Refactoring tagStormToTab to optionally handle csv output for cirm.
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    295608a714a87ed2400ad79d5a6749b0f1a6cde0 Mon Jun 5 13:08:52 2017 -0700
    oops. little fix to tagStorm cvs output.
• src/lib/uuid.c
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    ce3b570cf3c96344383503946cd71e05a2e29870 Fri Jun 9 11:57:35 2017 -0700
    Starting a local uuid module with makeUuidString.
• src/product/README.txt
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    f519936c321a3b8c80b806f9b1d4b07624991e66 Mon Jun 5 15:39:38 2017 -0700
    updating mirror manual to make it easier to read. no redmine yet
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/product/installer/README.md
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/product/installer/staticPage.html
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/product/mirrorDocs/staticPage.html
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/product/mirrorManual.txt
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    ab757a847cc78dd206a2bdce25c9a55151911812 Tue Jun 6 11:14:58 2017 -0700
    Bringing mirrr related markdown files back in order with the html they generate. Adding a message to mirror related docs to only edit the markdown version of the doc so the files don't get out of order. no refs
• src/tagStorm/tagStormArrayToCsv/tagStormArrayToCsv.c
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    d8b257c90191279ac9fcdea02f15f69b14f4315d Thu Jun 1 11:26:15 2017 -0700
    Downgrading debugging statements to verbose(2)
• src/tagStorm/tagStormReformat/tagStormReformat.c
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    409f0020af91f29da08f529db1b4bb95158db435 Thu Jun 8 23:29:43 2017 -0700
    Adding reverseStanzas option.
• src/tagStorm/tagStormToCsv/tagStormToCsv.c
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    045ffea66c916d05cb813b6751e3513ce979795d Sun Jun 4 12:09:56 2017 -0700
    Refactoring tagStormToTab to optionally handle csv output for cirm.
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    41f6340e8eaddf277cf1e5f42db46288547fffd3 Wed Jun 7 10:58:48 2017 -0700
    fixing typo in help tagStormToCsv
• src/utils/cgiSmokeTest
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    32010430d8ed0051465b8f4ced5383b050917799 Tue Jun 6 11:59:15 2017 -0700
    adding smoke test script, for Hiram, no redmine
• src/utils/makefile
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    489e3b9bd889b7ed2cb4f0619f8c8e7e0966b379 Tue Jun 6 11:59:54 2017 -0700
    adding smoke test script to makefile, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    225d6b42de62aa8a50848b8ddbabe281369c2832 Mon Jun 12 10:06:29 2017 -0700
    v351 preview1 refs #19473

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• files changed: 238