All File Changes

v356_base to v357_preview (2017-10-09 to 2017-10-16) v357

• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 3, context: html, text, full: html, text
    c80ad337d8e24c79da3a927a6c2a5f40c9251075 Fri Oct 13 16:44:15 2017 -0700
    CIRM: fixing missing extensions for tarballs submitted as unknown filetype
• src/hg/cirm/gateway/htdocs/cescgOrg.html
  • lines changed 78, context: html, text, full: html, text
    82f8f53ba1c4ff6858719ad659e71b5f47f63ead Fri Oct 13 09:19:53 2017 -0700
    Changing encoding of some characters and adding section for participating institutions on cescgOrg page. Correct name spelling and minor formatting change on cescgPeople page, no redmine
• src/hg/cirm/gateway/htdocs/cescgPeople.html
  • lines changed 10, context: html, text, full: html, text
    82f8f53ba1c4ff6858719ad659e71b5f47f63ead Fri Oct 13 09:19:53 2017 -0700
    Changing encoding of some characters and adding section for participating institutions on cescgOrg page. Correct name spelling and minor formatting change on cescgPeople page, no redmine
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 168, context: html, text, full: html, text
    eb3d9e9501a01515fa82d9e8aec5269a832538be Fri Oct 13 09:23:32 2017 -0700
    First pass at an updated help page. Very rough. Will improved soon. no redmine
• src/hg/hgCollection/hgCollection.c
  • lines changed 67, context: html, text, full: html, text
    957f2123050742982ef6c7aefcab70d29144924c Mon Oct 9 17:49:04 2017 -0700
    allow bedGraph. Change names in collections so they don't match names in trackDb, move the copying of custom tracks and collections to BEFORE the load of trackHubs, misc other bugs
  • lines changed 29, context: html, text, full: html, text
    93f1aea8db760b6d02766ab35413a0c3e2a63df8 Tue Oct 10 11:16:09 2017 -0700
    fix hgc clicks on custom tracks in collections
  • lines changed 3, context: html, text, full: html, text
    4ba031ce66aa01b97f23a82747b724a84cc94cb9 Tue Oct 10 13:53:51 2017 -0700
    add assembly to hgCollection title bar
  • lines changed 1, context: html, text, full: html, text
    d0f4fbf2ddcecf0f8b1d49575ab4c3ac10617b0d Wed Oct 11 14:39:06 2017 -0700
    change "Save" into Go button that saves and goes to hgTracks. Add wait screen for AJAX updates
  • lines changed 8, context: html, text, full: html, text
    1027c8e7702cdf5925a4db1fccdc81f9c64f8346 Wed Oct 11 18:44:52 2017 -0700
    fix new collection button, keep old track name in table name in trackDb for native tracks
• src/hg/hgGene/gad.c
  • lines changed 4, context: html, text, full: html, text
    3d72b973573f2db8c77f1a22f4e6852e2091c5d9 Fri Oct 13 22:20:12 2017 -0700
    Updating links to the CDC HuGE database resources. fixes #20317
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    e70a797121756d691b7559f71372c1955495eca1 Sun Oct 15 16:14:02 2017 -0700
    changed link to MGI for human only. refs 17415
• src/hg/hgTracks/bedGraph.c
  • lines changed 6, context: html, text, full: html, text
    957f2123050742982ef6c7aefcab70d29144924c Mon Oct 9 17:49:04 2017 -0700
    allow bedGraph. Change names in collections so they don't match names in trackDb, move the copying of custom tracks and collections to BEFORE the load of trackHubs, misc other bugs
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    93f1aea8db760b6d02766ab35413a0c3e2a63df8 Tue Oct 10 11:16:09 2017 -0700
    fix hgc clicks on custom tracks in collections
  • lines changed 9, context: html, text, full: html, text
    5fc4e4b808fce37ff781fd27d6782808ebbb5e92 Wed Oct 11 14:06:15 2017 -0700
    allowing trackDb statement dataVersion to be a file name, refs #20174
  • lines changed 4, context: html, text, full: html, text
    3d72b973573f2db8c77f1a22f4e6852e2091c5d9 Fri Oct 13 22:20:12 2017 -0700
    Updating links to the CDC HuGE database resources. fixes #20317
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    e5bca336b3a879884c7cd865cc2c1758e5ffbb3e Fri Oct 13 14:32:01 2017 -0700
    Check for NULL to support VCF files with missing header definitions.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 40, context: html, text, full: html, text
    d0a06fc54e95e7e8ee5bae3e04453d675eaf4abf Mon Oct 9 15:50:16 2017 -0700
    Adding some screens on uploading a hub to cyverse, refs #12822
  • lines changed 4, context: html, text, full: html, text
    e74e22d4df9f84743fcadf4f0012fde1b37d343b Thu Oct 12 14:51:41 2017 -0700
    Re-sizing cyverse images, refs #12822
  • lines changed 17, context: html, text, full: html, text
    9f4c4cf99363adbae924c834f439ee7dbf4d5843 Fri Oct 13 10:27:10 2017 -0700
    Updating hosting section after cyverse feedback, refs #12822
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 2, context: html, text, full: html, text
    5a800676097cf22902c80d1ae718527fab7e8364 Wed Oct 11 13:49:12 2017 -0700
    Adding grant reference National Human Genome Research Institute [U41-HG002371] to pubs.html page refs #20232
  • lines changed 4, context: html, text, full: html, text
    6c7ba2638004284318c0ed28f67af5bfe2f09dfa Thu Oct 12 16:47:48 2017 -0700
    Fixing bad url, no rm
• src/hg/htdocs/images/cyverseCreatePublicLink.png
  • lines changed 0, context: html, text, full: html, text
    d0a06fc54e95e7e8ee5bae3e04453d675eaf4abf Mon Oct 9 15:50:16 2017 -0700
    Adding some screens on uploading a hub to cyverse, refs #12822
• src/hg/htdocs/images/cyverseEditedPaths.png
  • lines changed 0, context: html, text, full: html, text
    d0a06fc54e95e7e8ee5bae3e04453d675eaf4abf Mon Oct 9 15:50:16 2017 -0700
    Adding some screens on uploading a hub to cyverse, refs #12822
  • lines changed 0, context: html, text, full: html, text
    9f4c4cf99363adbae924c834f439ee7dbf4d5843 Fri Oct 13 10:27:10 2017 -0700
    Updating hosting section after cyverse feedback, refs #12822
• src/hg/htdocs/images/cyverseSendToGenomeBrowser.png
  • lines changed 0, context: html, text, full: html, text
    d0a06fc54e95e7e8ee5bae3e04453d675eaf4abf Mon Oct 9 15:50:16 2017 -0700
    Adding some screens on uploading a hub to cyverse, refs #12822
• src/hg/htdocs/images/cyverseUploadButton.png
  • lines changed 0, context: html, text, full: html, text
    d0a06fc54e95e7e8ee5bae3e04453d675eaf4abf Mon Oct 9 15:50:16 2017 -0700
    Adding some screens on uploading a hub to cyverse, refs #12822
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 13, context: html, text, full: html, text
    c5f4f1ccec384b625eb128a89cd1fea35e45c5af Tue Oct 10 13:52:24 2017 -0700
    css changes in hgCollection
  • lines changed 37, context: html, text, full: html, text
    d0f4fbf2ddcecf0f8b1d49575ab4c3ac10617b0d Wed Oct 11 14:39:06 2017 -0700
    change "Save" into Go button that saves and goes to hgTracks. Add wait screen for AJAX updates
  • lines changed 3, context: html, text, full: html, text
    1027c8e7702cdf5925a4db1fccdc81f9c64f8346 Wed Oct 11 18:44:52 2017 -0700
    fix new collection button, keep old track name in table name in trackDb for native tracks
• src/hg/htdocs/staff.html
  • lines changed 4, context: html, text, full: html, text
    0a774f32ef9937970865eaddd9824851239189ca Tue Oct 10 08:18:57 2017 -0700
    moving ChrisE to alumni section
• src/hg/js/hgCollection.js
  • lines changed 23, context: html, text, full: html, text
    d0f4fbf2ddcecf0f8b1d49575ab4c3ac10617b0d Wed Oct 11 14:39:06 2017 -0700
    change "Save" into Go button that saves and goes to hgTracks. Add wait screen for AJAX updates
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    1027c8e7702cdf5925a4db1fccdc81f9c64f8346 Wed Oct 11 18:44:52 2017 -0700
    fix new collection button, keep old track name in table name in trackDb for native tracks
• src/hg/lib/cart.c
  • lines changed 8, context: html, text, full: html, text
    957f2123050742982ef6c7aefcab70d29144924c Mon Oct 9 17:49:04 2017 -0700
    allow bedGraph. Change names in collections so they don't match names in trackDb, move the copying of custom tracks and collections to BEFORE the load of trackHubs, misc other bugs
• src/hg/lib/gpFx.c
  • lines changed 2, context: html, text, full: html, text
    ec16665b0cbbc7f8e01992a65d328bee629b4e01 Fri Oct 13 15:01:12 2017 -0700
    Multi-base substitutions that straddled codon boundary were incompletely reported in {codon,aa}{Old,New} fields. fixes #20327
  • lines changed 2, context: html, text, full: html, text
    34b00a6ec9f42cc2c1d16e43e571c67e800e0604 Fri Oct 13 16:18:11 2017 -0700
    Fix error that caused insertion between splice site and the rest of the splice region to fall through the conditions for splice_region. fixes #20328.
• src/hg/lib/gtexEqtlTissue.as
  • lines changed 19, context: html, text, full: html, text
    51e5d640cf0700de6c9acb3c29ca61855943067f Tue Oct 10 11:30:08 2017 -0700
    gtexEqtlTissue.as is an exact duplicate of gtexEqtl.as. buildTableDescriptions finds and forbids duplicates. No other known dependencies on this new file yet. dropping with git rm. Kate can add it back when she returns.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 1, context: html, text, full: html, text
    ec16665b0cbbc7f8e01992a65d328bee629b4e01 Fri Oct 13 15:01:12 2017 -0700
    Multi-base substitutions that straddled codon boundary were incompletely reported in {codon,aa}{Old,New} fields. fixes #20327
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    957f2123050742982ef6c7aefcab70d29144924c Mon Oct 9 17:49:04 2017 -0700
    allow bedGraph. Change names in collections so they don't match names in trackDb, move the copying of custom tracks and collections to BEFORE the load of trackHubs, misc other bugs
  • lines changed 1, context: html, text, full: html, text
    8fe61f9fc004c6a92c95bae538d72853baffd3d1 Mon Oct 9 18:11:21 2017 -0700
    oops... need bedGraph in another if
• src/hg/lib/variantProjector.c
  • lines changed 4, context: html, text, full: html, text
    1c81d5ea61946f0fe68315a4679d68a4f3baf0f4 Fri Oct 13 17:00:50 2017 -0700
    Oops, forgot to reverse-complement shifted genomic sequence when transcript is on - strand. fixes #20329
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 4, context: html, text, full: html, text
    3c585f50db8af2da2ddeae705d13988f9e194636 Tue Oct 10 12:09:22 2017 -0700
    Minor style tweak to clinvar description page, refs #20268
  • lines changed 9, context: html, text, full: html, text
    cf74462533f7ccf9f288a839646f6daf0de3bcea Tue Oct 10 14:47:42 2017 -0700
    fixed three links that went offsite without target = _blank, and made a link to a paper all one piece, even though the partial title worked anyway
• src/hg/makeDb/trackDb/human/gad.html
  • lines changed 9, context: html, text, full: html, text
    3d72b973573f2db8c77f1a22f4e6852e2091c5d9 Fri Oct 13 22:20:12 2017 -0700
    Updating links to the CDC HuGE database resources. fixes #20317
• src/hg/makeDb/trackDb/human/hg19/gad.html
  • lines changed 95, context: html, text, full: html, text
    3d72b973573f2db8c77f1a22f4e6852e2091c5d9 Fri Oct 13 22:20:12 2017 -0700
    Updating links to the CDC HuGE database resources. fixes #20317
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.html
  • lines changed 1, context: html, text, full: html, text
    b7efda0a706ad91a2dfe1e84debce9d8f5652edb Wed Oct 11 16:56:21 2017 -0700
    Fixing minor typo in desc pg and moving eQTL tracks to reside side-by-side in Regulation, refs #15646
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.v1.ra
  • lines changed 2, context: html, text, full: html, text
    b7efda0a706ad91a2dfe1e84debce9d8f5652edb Wed Oct 11 16:56:21 2017 -0700
    Fixing minor typo in desc pg and moving eQTL tracks to reside side-by-side in Regulation, refs #15646
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e7ecff3477303685505d86a975cb6eac87128df2 Mon Oct 9 13:20:57 2017 -0700
    Staging GTEx eQTL Tissue composite v1 (with tables instead of files) on beta, refs #20236
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 20, context: html, text, full: html, text
    db909f40c4688c4c0fb05c5c3f708a4eb8586020 Tue Oct 10 13:58:25 2017 -0700
    Changing the priority of the tracks displayed in the bismap and umap super-tracks, refs #19154
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7958534dffa7f8d67a3975283002c8a1ecdc2d68 Tue Oct 10 16:14:41 2017 -0700
    adding special human override so new uniprot doesn't affect eboVir uniprot and removing superfluous spMut stanza, refs #20174
  • lines changed 1, context: html, text, full: html, text
    3b5bfab9a06246db7b0eb2016c1e209dbbf9ba1e Wed Oct 11 16:44:30 2017 -0700
    Changing clinvar shortlabel, refs #20268
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    11903d237166212634711841df63f8a8379be6e4 Wed Oct 11 08:52:33 2017 -0700
    Fixing broken links found by then broken link report for braFlo1, no redmine.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    7958534dffa7f8d67a3975283002c8a1ecdc2d68 Tue Oct 10 16:14:41 2017 -0700
    adding special human override so new uniprot doesn't affect eboVir uniprot and removing superfluous spMut stanza, refs #20174
  • lines changed 1, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/uniprot.html
  • lines changed 37, context: html, text, full: html, text
    a409e830ae5c049aae9015e98aba82b186000cc0 Wed Oct 11 11:05:15 2017 -0700
    now that uniprot track is released, add back the temp file remove commands, and adding Chris to the track desc page, refs #20174
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0b1b2cc95f4056aa5740d1bd600c12140b8da299 Wed Oct 11 08:30:24 2017 -0700
    Woops forgot to add bigDataUrl to organism specific overrides, also making uniprot public, refs #20174
• src/hg/pslSelect/pslSelect.c
  • lines changed 47, context: html, text, full: html, text
    c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700
    changing pslSelect for uniprot track, refs #20174
• src/hg/pslSelect/tests/expected/queryPairs2.out.psl
  • lines changed 3, context: html, text, full: html, text
    c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700
    changing pslSelect for uniprot track, refs #20174
• src/hg/pslSelect/tests/input/queryPairs2.in.psl
  • lines changed 5, context: html, text, full: html, text
    c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700
    changing pslSelect for uniprot track, refs #20174
• src/hg/pslSelect/tests/input/queryPairs2.queries
  • lines changed 3, context: html, text, full: html, text
    c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700
    changing pslSelect for uniprot track, refs #20174
• src/hg/pslSelect/tests/makefile
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    c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700
    changing pslSelect for uniprot track, refs #20174
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 320, context: html, text, full: html, text
    540240320f4ee3729ca01c626f086a2bd0a3a782 Mon Oct 9 19:00:17 2017 -0700
    adding version 90 definitions refs #20304
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    b4538cf2c8dac8959be52d03fc015f214b23e4ad Tue Oct 10 13:14:01 2017 -0700
    the criGri1 is actually criGriChoV1 refs #20304
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    f6fcab704fe71ebda4159ee593a0da9b3c071882 Tue Oct 10 16:18:02 2017 -0700
    fixup dipOrd and susScr names refs #20304
• src/hg/utils/automation/chromAlias.pl
  • lines changed 1, context: html, text, full: html, text
    2aa51d9f0a6561c7166e297b57a6d7dd5361351c Fri Oct 13 15:05:20 2017 -0700
    fix small error in input file verification refs #20304
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 57, context: html, text, full: html, text
    fd74797404b4f5ed1ef223464bf9458c5edcfb96 Tue Oct 10 08:15:15 2017 -0700
    fixup check for identical to previous and enable debug mode refs #20304
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    0870ef2f581b039c62a512fb4a7a5566924299b2 Wed Oct 11 11:05:01 2017 -0700
    correctly load ensemblGeneScaffold table add checkTableCoords for that an ensGene tables refs #20304
• src/hg/utils/otto/README.md
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    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 3, context: html, text, full: html, text
    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
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    b36c36e95e76f131b6fc05719fd3d39df585cfed Tue Oct 10 14:58:58 2017 -0700
    fixing features with names that are just a number, refs #20268
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    379ae9b004b804fac2cb1681934c9c33d7250a2c Wed Oct 11 17:37:18 2017 -0700
    fixing number-only names in clinvar, refs #20268
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    5d06774aa3598b4b5cba29ba426c9b79f6967c28 Thu Oct 12 11:08:56 2017 -0700
    another fix for clinvar again, refs #20268
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    23f219ade6005831496b8e31507cdeab988dd8ae Thu Oct 12 12:44:21 2017 -0700
    shortening a few very long labels in clinvar, refs #20268
• src/hg/utils/otto/uniprot/README.txt
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    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
• src/hg/utils/otto/uniprot/doUniprot
  • lines changed 680, context: html, text, full: html, text
    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
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    c023499db31b1b6f72eb83f3ccb76b239d81d0c0 Tue Oct 10 16:08:27 2017 -0700
    creating uniprot version file for Jorges auto archiver now at the very very end of the pipeline, refs #20268
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    a409e830ae5c049aae9015e98aba82b186000cc0 Wed Oct 11 11:05:15 2017 -0700
    now that uniprot track is released, add back the temp file remove commands, and adding Chris to the track desc page, refs #20174
  • lines changed 2, context: html, text, full: html, text
    5fc4e4b808fce37ff781fd27d6782808ebbb5e92 Wed Oct 11 14:06:15 2017 -0700
    allowing trackDb statement dataVersion to be a file name, refs #20174
• src/hg/utils/otto/uniprot/makeUniProtPsl.sh
  • lines changed 127, context: html, text, full: html, text
    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
  • lines changed 1, context: html, text, full: html, text
    a409e830ae5c049aae9015e98aba82b186000cc0 Wed Oct 11 11:05:15 2017 -0700
    now that uniprot track is released, add back the temp file remove commands, and adding Chris to the track desc page, refs #20174
• src/hg/utils/otto/uniprot/makefile
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    a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700
    fixing stray files in uniprot, refs #20174
• src/hg/utils/uniprotMutations/README.txt
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    c643ac79e685df447f830a72d6a4bda6cb57014c Tue Oct 10 15:29:07 2017 -0700
    removing the old clinvar pipeline, refs #20268
• src/hg/utils/uniprotMutations/liftUniprotMut.py
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    c643ac79e685df447f830a72d6a4bda6cb57014c Tue Oct 10 15:29:07 2017 -0700
    removing the old clinvar pipeline, refs #20268
• src/hg/utils/uniprotMutations/load.sh
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    c643ac79e685df447f830a72d6a4bda6cb57014c Tue Oct 10 15:29:07 2017 -0700
    removing the old clinvar pipeline, refs #20268
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
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    1c81d5ea61946f0fe68315a4679d68a4f3baf0f4 Fri Oct 13 17:00:50 2017 -0700
    Oops, forgot to reverse-complement shifted genomic sequence when transcript is on - strand. fixes #20329
• src/utils/git-reports/git-reports.c
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    f72c889501d893c6bbddead5cf9cdea4e6e29810 Wed Oct 11 17:21:38 2017 -0700
    Fixing bug in git-reports discovered by Hiram. When whitespace-only diff occurs, the parent paths end up not being created.
• src/utils/git-reports/makefile
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    f72c889501d893c6bbddead5cf9cdea4e6e29810 Wed Oct 11 17:21:38 2017 -0700
    Fixing bug in git-reports discovered by Hiram. When whitespace-only diff occurs, the parent paths end up not being created.
• src/utils/qa/weeklybld/buildEnv.csh
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    f997b0b61349d1df9623cf206a8125982149ee4f Mon Oct 16 10:12:48 2017 -0700
    v357 preview1 refs #20233
• src/utils/uniprotToTab
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    cb3f1b0b44201216b5cdb2b89b6da201dc1c1f48 Tue Oct 10 09:20:47 2017 -0700
    fixing the UniProt parser for Regeneron, refs #20174
• src/utils/webSync
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    1ac3db7f3d267c2852d42da712976fe2d962809a Mon Oct 9 13:03:50 2017 -0700
    CIRM: allowing symlinks in the little webSync tool

• lines changed: 2736
• files changed: 95