All File Changes

v356_preview2 to v356_base (2017-10-02 to 2017-10-09) v356

• src/hg/hgCollection/hgCollection.c
  • lines changed 129, context: html, text, full: html, text
    8dc2f2a3bfe8d47e02a94ca4d9f62063df86b15c Thu Oct 5 14:56:25 2017 -0700
    ongoing work on hgCollection. Add the ability to add tracks in hgTracks to a collection. Turn "overlay method" back on for custom collections. Fix panning bug in hgTracks with custom collections
  • lines changed 2, context: html, text, full: html, text
    2c94ab76e8582c89539e432235cc0d0af2bba841 Fri Oct 6 11:22:24 2017 -0700
    response to code review #20250
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 3, context: html, text, full: html, text
    7a3a9c41b9f6b37c339f5b79cb8140fb16025b5d Thu Oct 5 15:11:28 2017 -0700
    changing interaction viewer hgGene link, refs #19454
• src/hg/hgTracks/extTools.c
  • lines changed 12, context: html, text, full: html, text
    efd06ae9f3a86f106ac1a8b3b633f384a1a223fe Wed Oct 4 12:38:47 2017 -0700
    allowing extTools.ra to live outside the cgi-bin directory
• src/hg/hgTracks/hgTracks.c
  • lines changed 17, context: html, text, full: html, text
    8dc2f2a3bfe8d47e02a94ca4d9f62063df86b15c Thu Oct 5 14:56:25 2017 -0700
    ongoing work on hgCollection. Add the ability to add tracks in hgTracks to a collection. Turn "overlay method" back on for custom collections. Fix panning bug in hgTracks with custom collections
• src/hg/hgTracks/multiWig.c
  • lines changed 2, context: html, text, full: html, text
    8dc2f2a3bfe8d47e02a94ca4d9f62063df86b15c Thu Oct 5 14:56:25 2017 -0700
    ongoing work on hgCollection. Add the ability to add tracks in hgTracks to a collection. Turn "overlay method" back on for custom collections. Fix panning bug in hgTracks with custom collections
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    9c0eb75906adbead8c25abf527b5e687271d5eec Mon Oct 9 09:46:24 2017 -0700
    Adding note about udcTimeout to custom track help page, refs #9700
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 0, context: html, text, full: html, text
    f7882b4bcd58ae40339d297462342bc3d06cbfa6 Fri Oct 6 09:08:56 2017 -0700
    Correcting some indentation in an example that was lost when we did sytle revamps
• src/hg/htdocs/images/Eulemur_flavifrons,jpg
  • lines changed 0, context: html, text, full: html, text
    845bd7c6663afa7a97050c97d21ddaee40b1b946 Mon Oct 2 14:10:40 2017 -0700
    photo from David Haring/Duke Lemur Center refs #20265
• src/hg/htdocs/images/Eulemur_flavifrons.jpg
  • lines changed 0, context: html, text, full: html, text
    6618ddc09ac5153aeabba20bd38c7088e88ba3da Mon Oct 2 14:18:16 2017 -0700
    photo from David Haring/Duke Lemur Center refs #20265
• src/hg/htdocs/images/Eulemur_macaco.jpg
  • lines changed 0, context: html, text, full: html, text
    8718acc2eff6cede487bbbdf3117c897700d0591 Mon Oct 2 14:47:55 2017 -0700
    photo from David Haring/Duke Lemur Center refs #20266
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    772d174923bdc3f16ce1b8f8f2b5c4500e59c36a Tue Oct 3 17:46:16 2017 -0700
    Updating news date from code review
• src/hg/inc/gtexEqtlCluster.h
  • lines changed 1, context: html, text, full: html, text
    ec903ae4d17d39e1d3ca0490fcbe7c0e061edd5e Wed Oct 4 16:48:16 2017 -0700
    Correct definition of CAVIAR probability; input from Casey Brown, U Penn (GTEx analyst). refs #15646
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    8248a721c03198c87194c2c684685d395df82847 Mon Oct 9 10:00:06 2017 -0700
    New version number v356
• src/hg/js/dbDbTaxonomy.js
  • lines changed 24, context: html, text, full: html, text
    93fabb375cf33bd956ebae16abf80200ccdb9b5c Fri Oct 6 13:24:47 2017 -0700
    adding cerAty1 manLeu1 aotNan1 cebCap1 micMur1 proCoq1 eulMac1 eulFla1 lepWed1 neoSch1 refs #20190 #20196 #20237 #18984 #20235 #20266 #20265 #19883
• src/hg/js/hgCollection.js
  • lines changed 1, context: html, text, full: html, text
    2c94ab76e8582c89539e432235cc0d0af2bba841 Fri Oct 6 11:22:24 2017 -0700
    response to code review #20250
• src/hg/js/hgTracks.js
  • lines changed 60, context: html, text, full: html, text
    8dc2f2a3bfe8d47e02a94ca4d9f62063df86b15c Thu Oct 5 14:56:25 2017 -0700
    ongoing work on hgCollection. Add the ability to add tracks in hgTracks to a collection. Turn "overlay method" back on for custom collections. Fix panning bug in hgTracks with custom collections
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 2, context: html, text, full: html, text
    d9f2be9bd1b2d47dbe93df2cdbe1731f06d42980 Wed Oct 4 11:05:58 2017 -0700
    Oops, forgot to hook up update function so Modal's remove button did not work until it had contents. refs #20272
• src/hg/lib/gtexEqtl.as
  • lines changed 1, context: html, text, full: html, text
    ec903ae4d17d39e1d3ca0490fcbe7c0e061edd5e Wed Oct 4 16:48:16 2017 -0700
    Correct definition of CAVIAR probability; input from Casey Brown, U Penn (GTEx analyst). refs #15646
  • lines changed 1, context: html, text, full: html, text
    5bdc0c1e3a2e6a4bccc42597fd123ef594a634ce Thu Oct 5 14:55:00 2017 -0700
    Fix 95% set definition again, as per Farhad Hormozdiari (author of CAVIAR). refs #15646
• src/hg/lib/gtexEqtl.sql
  • lines changed 1, context: html, text, full: html, text
    ec903ae4d17d39e1d3ca0490fcbe7c0e061edd5e Wed Oct 4 16:48:16 2017 -0700
    Correct definition of CAVIAR probability; input from Casey Brown, U Penn (GTEx analyst). refs #15646
  • lines changed 1, context: html, text, full: html, text
    5bdc0c1e3a2e6a4bccc42597fd123ef594a634ce Thu Oct 5 14:55:00 2017 -0700
    Fix 95% set definition again, as per Farhad Hormozdiari (author of CAVIAR). refs #15646
• src/hg/lib/gtexEqtlCluster.as
  • lines changed 1, context: html, text, full: html, text
    ec903ae4d17d39e1d3ca0490fcbe7c0e061edd5e Wed Oct 4 16:48:16 2017 -0700
    Correct definition of CAVIAR probability; input from Casey Brown, U Penn (GTEx analyst). refs #15646
• src/hg/lib/gtexEqtlCluster.sql
  • lines changed 1, context: html, text, full: html, text
    ec903ae4d17d39e1d3ca0490fcbe7c0e061edd5e Wed Oct 4 16:48:16 2017 -0700
    Correct definition of CAVIAR probability; input from Casey Brown, U Penn (GTEx analyst). refs #15646
• src/hg/lib/gtexEqtlTissue.as
  • lines changed 19, context: html, text, full: html, text
    dbf690a43c2a57d780e7f6327ca9246b54e7904a Thu Oct 5 15:49:25 2017 -0700
    Add v1 GTEx eQTL tracks. refs #15646
• src/hg/lib/gtexUi.c
  • lines changed 1, context: html, text, full: html, text
    13f8d3e2777e895b5c59af59fb6afad03ad58dbb Wed Oct 4 16:46:46 2017 -0700
    Change config labeling to be clearer. Thanks Cath. refs #15646
• src/hg/lib/hAnno.c
  • lines changed 28, context: html, text, full: html, text
    c95bb9d37e9231523edeff445f1951f48d4a7046 Wed Oct 4 11:08:02 2017 -0700
    hAnno.c did not yet recognize bigPsl -- since I anticipate more bigBed-based big* types in the future, I'll assume any big* that's not bigWig is bigBed-based. refs #20272
• src/hg/makeDb/doc/eulFla1/initialBuild.txt
  • lines changed 755, context: html, text, full: html, text
    8004fa20b262bb782228261a6370a6623d9eeca2 Mon Oct 2 14:32:31 2017 -0700
    running up repeatMasker refs #20265
  • lines changed 148, context: html, text, full: html, text
    dac22096644161f9f3fc43e447726b17fddaa652 Tue Oct 3 14:59:25 2017 -0700
    running genbank and lastz hg38 mm10 refs #20265
  • lines changed 74, context: html, text, full: html, text
    27b7db1cb0d4b9f16270a7d3bf7f0eed6f6ddc0f Fri Oct 6 13:05:49 2017 -0700
    completed and in pushQ refs #20265
• src/hg/makeDb/doc/eulMac1/initialBuild.txt
  • lines changed 708, context: html, text, full: html, text
    6ff3a348c93096e43256b2464f44a233849e1fca Fri Oct 6 13:09:49 2017 -0700
    complete and in pushQ refs #20266
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 139, context: html, text, full: html, text
    d6dad1d758703e6d95d8b48773dd6233ff5c052d Tue Oct 3 13:07:17 2017 -0700
    finish off lastz chainNet runs for cerAty1 proCoq1 cebCap1 refs #20199 #20235 #20237
  • lines changed 138, context: html, text, full: html, text
    ad55d247b89abf49a41959a7afa9e393c8afa4a2 Fri Oct 6 08:22:34 2017 -0700
    completed lastz/chainNet runs for eulFla1 and eulMac1 refs #20265 #20266
• src/hg/makeDb/doc/mm10.txt
  • lines changed 18, context: html, text, full: html, text
    d6dad1d758703e6d95d8b48773dd6233ff5c052d Tue Oct 3 13:07:17 2017 -0700
    finish off lastz chainNet runs for cerAty1 proCoq1 cebCap1 refs #20199 #20235 #20237
  • lines changed 114, context: html, text, full: html, text
    68ebe6fd2404b559a4eef5794784e56c3970aac6 Wed Oct 4 15:56:14 2017 -0700
    running up cebCap1 and eulMac1 lastz/chainNet refs #20237 #20265
  • lines changed 65, context: html, text, full: html, text
    0bc02574b0f890fd2e1a1dead2e84b4eaba123c4 Fri Oct 6 08:21:59 2017 -0700
    completed lastz/chainNet runs for cebCap1, eulFla1, eulMac1 refs #20265 #20266 #20237
• src/hg/makeDb/doc/proCoq1/initialBuild.txt
  • lines changed 170, context: html, text, full: html, text
    0279b1f1a884ea9271a62592dbbd4c580fa3513b Thu Oct 5 11:37:01 2017 -0700
    completed, in the pushQ refs #20235
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    f02549bd0ec06ce5ff5d4da0a1261bbf04c0962a Wed Oct 4 15:49:13 2017 -0700
    Added eulFla1 - Sclater's lemur - Eulemur flavifrons refs #20265
  • lines changed 1, context: html, text, full: html, text
    2dabf9bf784322465f55f3b457236a1a7170af75 Wed Oct 4 21:14:29 2017 -0700
    Added eulMac1 - Black lemur - Eulemur macaco refs #20266
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 42, context: html, text, full: html, text
    2144cef3d22ded907c6430ac1eef40bce59576c8 Tue Oct 3 14:55:36 2017 -0700
    adding eulFla1 and eulMac1 refs #20265 #20266
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    f02549bd0ec06ce5ff5d4da0a1261bbf04c0962a Wed Oct 4 15:49:13 2017 -0700
    Added eulFla1 - Sclater's lemur - Eulemur flavifrons refs #20265
  • lines changed 1, context: html, text, full: html, text
    2dabf9bf784322465f55f3b457236a1a7170af75 Wed Oct 4 21:14:29 2017 -0700
    Added eulMac1 - Black lemur - Eulemur macaco refs #20266
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 4, context: html, text, full: html, text
    2144cef3d22ded907c6430ac1eef40bce59576c8 Tue Oct 3 14:55:36 2017 -0700
    adding eulFla1 and eulMac1 refs #20265 #20266
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 4, context: html, text, full: html, text
    0822a62eb01e4d6b04c2b8816f1070cc0b25b9e4 Thu Oct 5 15:35:20 2017 -0700
    Make err message more informative.
• src/hg/makeDb/schema/all.joiner
  • lines changed 11, context: html, text, full: html, text
    85e602552695078b2003350fb23235049c2797e9 Tue Oct 3 13:32:14 2017 -0700
    adding proCoq1 rules refs #20235
  • lines changed 12, context: html, text, full: html, text
    fb84b31e56fb500e71a9622d9756e75f7184f13e Fri Oct 6 08:11:12 2017 -0700
    adding rules for eulFla1 and eulMac1 refs #20265 #20266
• src/hg/makeDb/trackDb/ccdsGene.html
  • lines changed 1, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 10, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/drosophila/bdtnpChipperOld.html
  • lines changed 2, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevSignal.html
  • lines changed 3, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/affyDrosDevTransfrags.html
  • lines changed 3, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/augustus.html
  • lines changed 4, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
  • lines changed 6, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/flyreg2.html
  • lines changed 4, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 3, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
  • lines changed 1, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/est.html
  • lines changed 1, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/evofold.html
  • lines changed 6, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/refGene.html
  • lines changed 3, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/drosophila/xenoMrna.html
  • lines changed 2, context: html, text, full: html, text
    1796b938926341bf3a6cee66553201d75359d148 Mon Oct 2 14:13:36 2017 -0700
    Fixing broken links found by the broken link report for dm2, no Redmine
• src/hg/makeDb/trackDb/gorilla/gorGor5/description.html
  • lines changed 1, context: html, text, full: html, text
    f95cc28fb6c730509dc38a2b1d28ff5d455a1232 Thu Oct 5 08:49:01 2017 -0700
    correct GCA identifier refs #17580
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 6, context: html, text, full: html, text
    269abeff2abc4babb9acdfd616d7c2eae8d96c04 Tue Oct 3 11:47:19 2017 -0700
    adapting the clinvar track, refs #20268
  • lines changed 6, context: html, text, full: html, text
    ad3a64df6c3377bcc18104285d65ccc6a6f43182 Tue Oct 3 15:20:42 2017 -0700
    adding better clinVar mouseover and star rating filter, refs #20268
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.html
  • lines changed 15, context: html, text, full: html, text
    59687fa0ffebfc93647a852ef2611d2ceb4e4f46 Wed Oct 4 16:32:45 2017 -0700
    Minor edits and clarification of CAVIAR probability/credible set from Casey Brown, U Penn (GTEx analyst). refs #15646
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    0822a62eb01e4d6b04c2b8816f1070cc0b25b9e4 Thu Oct 5 15:35:20 2017 -0700
    Make err message more informative.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 1, context: html, text, full: html, text
    dbf690a43c2a57d780e7f6327ca9246b54e7904a Thu Oct 5 15:49:25 2017 -0700
    Add v1 GTEx eQTL tracks. refs #15646
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.v1.ra
  • lines changed 415, context: html, text, full: html, text
    0822a62eb01e4d6b04c2b8816f1070cc0b25b9e4 Thu Oct 5 15:35:20 2017 -0700
    Make err message more informative.
  • lines changed 1, context: html, text, full: html, text
    ab836673776cc8476c5c49fa833954fbae3beba0 Thu Oct 5 16:01:04 2017 -0700
    Fix vis on new track. refs #15646
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    523b2181eb7807acce087148972d4e2ac2bd9a74 Mon Oct 2 14:47:41 2017 -0700
    Releasing v.0 GTEx eQTL tracks for hg19, refs #20236
  • lines changed 2, context: html, text, full: html, text
    0822a62eb01e4d6b04c2b8816f1070cc0b25b9e4 Thu Oct 5 15:35:20 2017 -0700
    Make err message more informative.
  • lines changed 0, context: html, text, full: html, text
    dbf690a43c2a57d780e7f6327ca9246b54e7904a Thu Oct 5 15:49:25 2017 -0700
    Add v1 GTEx eQTL tracks. refs #15646
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 42, context: html, text, full: html, text
    8ed96de4f65a08f9209cced8dbada9a17c3c49d7 Fri Oct 6 15:10:39 2017 -0700
    Making the bismap and umap track names lowercase to match our naming convention for tracks, refs #19154
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 4, context: html, text, full: html, text
    8ce93daf30f247c13ae4be150055fff7dfa437d0 Wed Oct 4 15:10:27 2017 -0700
    added a description to clarify meaning of item names
• src/hg/makeDb/trackDb/human/snpedia.html
  • lines changed 36, context: html, text, full: html, text
    43a51bfe58571dc017312986be00c05c48d14829 Fri Oct 6 11:31:23 2017 -0700
    Releasing SNPedia to hg19 & hg38, refs #19811
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    269abeff2abc4babb9acdfd616d7c2eae8d96c04 Tue Oct 3 11:47:19 2017 -0700
    adapting the clinvar track, refs #20268
  • lines changed 2, context: html, text, full: html, text
    ad3a64df6c3377bcc18104285d65ccc6a6f43182 Tue Oct 3 15:20:42 2017 -0700
    adding better clinVar mouseover and star rating filter, refs #20268
  • lines changed 5, context: html, text, full: html, text
    43a51bfe58571dc017312986be00c05c48d14829 Fri Oct 6 11:31:23 2017 -0700
    Releasing SNPedia to hg19 & hg38, refs #19811
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700
    adding eulFal1 to the browser refs #20265
  • lines changed 1, context: html, text, full: html, text
    ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700
    adding eulMac1 to the browser refs #20266
• src/hg/makeDb/trackDb/mouse/FaceBase24SampleTypesAvg.html
  • lines changed 5, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/jaxQtl.html
  • lines changed 1, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 4, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli6.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/mouse/snp142.shared.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/patSeq.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/primate/eulFla1/description.html
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    fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700
    adding eulFal1 to the browser refs #20265
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    3027fa667b573f3b541458ae6e5c1aebae19a88c Mon Oct 2 14:28:20 2017 -0700
    correct reference to David Haring/Duke Primate Center for the photograph refs #20265
• src/hg/makeDb/trackDb/primate/eulFla1/gap.html
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    fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700
    adding eulFal1 to the browser refs #20265
• src/hg/makeDb/trackDb/primate/eulFla1/gold.html
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    fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700
    adding eulFal1 to the browser refs #20265
• src/hg/makeDb/trackDb/primate/eulFla1/trackDb.ra
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    fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700
    adding eulFal1 to the browser refs #20265
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    19736a52d7a9faa57f2f4aa6de3cf0f6d29d346b Tue Oct 3 14:27:39 2017 -0700
    adding gold assembly table search rule refs #20265
• src/hg/makeDb/trackDb/primate/eulMac1/description.html
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    ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700
    adding eulMac1 to the browser refs #20266
• src/hg/makeDb/trackDb/primate/eulMac1/gap.html
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    ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700
    adding eulMac1 to the browser refs #20266
• src/hg/makeDb/trackDb/primate/eulMac1/gold.html
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    ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700
    adding eulMac1 to the browser refs #20266
• src/hg/makeDb/trackDb/primate/eulMac1/trackDb.ra
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    ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700
    adding eulMac1 to the browser refs #20266
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    beb04dc638d72f491110d6ef62e5de61b170c6bf Wed Oct 4 20:59:41 2017 -0700
    adding gold assembly track search rule refs #20266
• src/hg/makeDb/trackDb/qPcrPrimers.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/snp137.shared.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/snp138.shared.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    ca284af0214e4b692e906fc368bf245b863ae900 Mon Oct 2 11:47:58 2017 -0700
    uniprot adding subtrack, refs #20174
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    72bbf2bbf1d1c3e07c7bc7f38880975006b7421c Tue Oct 3 09:21:49 2017 -0700
    fixing order issue in uniprot track, refs #20174
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    efd06ae9f3a86f106ac1a8b3b633f384a1a223fe Wed Oct 4 12:38:47 2017 -0700
    allowing extTools.ra to live outside the cgi-bin directory
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    775a0e7e51a9a56dec72e48c74c645237ed0985b Wed Oct 4 14:05:36 2017 -0700
    changing uniprot track name, refs #10174
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    15f739762a3d3cdfd9b9e367f025849787644814 Wed Oct 4 14:56:25 2017 -0700
    fixing uniprot track search, refs #20174
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    3405765d68f5ce7c202ccae6b7be2e9b4e1aaae3 Thu Oct 5 11:19:34 2017 -0700
    adding missing searchindex for trembl, refs #10174
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    e5af91bfa1cea67bb91f21f1dda24b2c47acee89 Thu Oct 5 14:50:27 2017 -0700
    uniprot another search index field missing
• src/hg/makeDb/trackDb/uniprot.html
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    ca284af0214e4b692e906fc368bf245b863ae900 Mon Oct 2 11:47:58 2017 -0700
    uniprot adding subtrack, refs #20174
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    97ec216845aa44b08cb7a5d7229274e8754ef61d Wed Oct 4 16:39:00 2017 -0700
    fixing typo on uniprot description page, refs #20252
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    eace73563d5511332897cea83a4a4fe27ebba184 Wed Oct 4 16:47:22 2017 -0700
    fixing link to source code, refs #20174
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    0dd99f31c7ff9124951ac417344e25ddf88c092e Thu Oct 5 16:52:48 2017 -0700
    Fixing up description page colors to match the current version of the uniprot track, refs #20174
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
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    f000eda7a532e6a2b6cedebdeefa18b72a41a9fc Thu Oct 5 11:31:30 2017 -0700
    Fixing broken links found by the broken link report for mm10, no redmine
• src/hg/utils/automation/makeGenomeDb.pl
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    466229ba187359d68a2c8c3047da4a3705f1bba7 Mon Oct 2 14:07:07 2017 -0700
    correctly escape organism common name that my have single quote marks refs #20265
• src/hg/utils/gff3ToGenePred/tests/expected/mm10GencodeTest.attrs
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/gff3ToGenePred/tests/expected/mm10GencodeTest.gp
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/gff3ToGenePred/tests/expected/nameAttrNameTest.attrs
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/gff3ToGenePred/tests/expected/useNameTest.attrs
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/gff3ToGenePred/tests/input/mm10Gencode.gff3
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/gff3ToGenePred/tests/makefile
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    4d34c553439377b296f1487d764c74c09ad43810 Wed Oct 4 23:47:19 2017 -0700
    added some test cases for attributes
• src/hg/utils/otto/clinvar/clinVarToBed
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    269abeff2abc4babb9acdfd616d7c2eae8d96c04 Tue Oct 3 11:47:19 2017 -0700
    adapting the clinvar track, refs #20268
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    ad3a64df6c3377bcc18104285d65ccc6a6f43182 Tue Oct 3 15:20:42 2017 -0700
    adding better clinVar mouseover and star rating filter, refs #20268
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    797c270cbde0dbce5db0ea6e07ec7b2c7e6e3773 Wed Oct 4 14:54:53 2017 -0700
    fixing error on empty fields, refs #20268
• src/hg/utils/transMapPslToGenePred/tests/expected/cds2InsertTest.mapped.gp
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
    correctly handle CDS gap closing when there is an insertion in the genome
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/expected/fill30Test.mapped.gp
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
    correctly handle CDS gap closing when there is an insertion in the genome
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest30.mapped.gp
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
    correctly handle CDS gap closing when there is an insertion in the genome
• src/hg/utils/transMapPslToGenePred/tests/input/chimp.mapped.psl
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
    correctly handle CDS gap closing when there is an insertion in the genome
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/input/chimp.src.gp
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/tests/makefile
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
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    15cda765912e9420345a2064ce0ab94925d4a3d9 Mon Oct 2 23:20:12 2017 -0700
    updated test result and added a test
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    5b5d272fab3ad3385a7b4069e35993f4571ccd7d Mon Oct 2 12:02:24 2017 -0700
    correctly handle CDS gap closing when there is an insertion in the genome
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    93ca761b2f6f6c010203502ea22f569ab460d4c8 Tue Oct 3 12:21:22 2017 -0700
    fixed typo
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    8e1263f6d7474b51d69d4560fe4f548675b12c5b Tue Oct 3 12:26:17 2017 -0700
    improved comment (testing redmine)
• src/lib/htmshell.c
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    3f650c754a49fd4a0f5455adb89599b38ac2d88f Wed Oct 4 14:43:13 2017 -0700
    fixing stray bullet point in warnings, refs #20274
• src/utils/qa/weeklybld/buildEnv.csh
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    34695ee6ca36f4c18fc24392bce919548618b322 Mon Oct 9 09:59:18 2017 -0700
    v356 final build refs ##20233

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