All File Changes

v352_preview2 to v352_base (2017-07-10 to 2017-07-17) v352

• src/hg/hgGeneGraph/hgGeneGraph
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    cf32bd93dfcf0e307c889aaef4e5b1845bbd5a98 Tue Jul 11 17:55:00 2017 -0700
    Adding support for GBIB-style remote /gbdb files to hgGeneGraph. refs #19745
• src/hg/hgTracks/gtexEqtlClusterTrack.c
  • lines changed 85, context: html, text, full: html, text
    5b1a4883cd3c9d4be801592648d729a394e07240 Mon Jul 10 15:31:42 2017 -0700
    Add indicator of tissue color to eQTL right label for single-tissue items. refs #15646
• src/hg/hgTracks/peptideAtlasTrack.c
  • lines changed 1, context: html, text, full: html, text
    0384fa0a17672e37966d89532192e9f61352c7cd Tue Jul 11 10:57:36 2017 -0700
    Restore order of linked feature components after codon translation. Fixes bug with label display of split codons in pack mode. refs #19634
• src/hg/hgc/gtexEqtlClusterClick.c
  • lines changed 27, context: html, text, full: html, text
    0a9a2e76325358ac6a0f15040766e1f9a8a327ff Tue Jul 11 14:34:46 2017 -0700
    Add some links out and details from SNP and GWAS tracks. refs #1646
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 3, context: html, text, full: html, text
    65049ed7ff4fd61f9bd03aa9d3ca99c83b1d5337 Fri Jul 14 09:22:57 2017 -0700
    Adding explicit location of folders directory for assembly hubs on gbib for mlq, refs #19792
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    3783a7936f79711cf6ee9de8ca34a2459a3bb232 Fri Jul 14 14:04:11 2017 -0700
    announcing new video on Multi-Region mode BED file load
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    c14e2f319c0c9c78f90d193561e546ae55c1501b Fri Jul 14 15:06:00 2017 -0700
    Announcing the alternative mouse strains hub and the Mouse SNPs track, refs #13553 and #18305
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    b6632e02e55780f5ef4be39dce12eb527271f477 Fri Jul 14 15:17:48 2017 -0700
    Changing a preposition, refs #13553
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    66370cc34062bc22323ceb3a1db1d87579baaa66 Fri Jul 14 15:26:42 2017 -0700
    Cleaning up the announcement a bit more by removing redundancy, refs #13553
• src/hg/htdocs/images/training/vidTitle11.jpg
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    a177ba5bbd68ad6ada973378c2144635557887b2 Fri Jul 14 12:49:51 2017 -0700
    adding new video and links to it
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 8, context: html, text, full: html, text
    c6f3f198024402001d6dd0ba8a6460f06df6d363 Wed Jul 12 10:03:24 2017 -0700
    Removing Note that was added to share about hgdownload going to genome per CR and input, ref #19626 #19770
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    19499cd57c11fecf8ae29bef0a8b39be00de9976 Wed Jul 12 16:46:55 2017 -0700
    removed comments around the genome-announce Subscribe link to enable it
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    3783a7936f79711cf6ee9de8ca34a2459a3bb232 Fri Jul 14 14:04:11 2017 -0700
    announcing new video on Multi-Region mode BED file load
  • lines changed 1, context: html, text, full: html, text
    71f1181f005f401f50738f38531936f203cbb55f Fri Jul 14 14:07:47 2017 -0700
    shortened title of news item
  • lines changed 13, context: html, text, full: html, text
    c14e2f319c0c9c78f90d193561e546ae55c1501b Fri Jul 14 15:06:00 2017 -0700
    Announcing the alternative mouse strains hub and the Mouse SNPs track, refs #13553 and #18305
• src/hg/htdocs/training/index.html
  • lines changed 11, context: html, text, full: html, text
    a177ba5bbd68ad6ada973378c2144635557887b2 Fri Jul 14 12:49:51 2017 -0700
    adding new video and links to it
• src/hg/htdocs/training/vids/index.html
  • lines changed 85, context: html, text, full: html, text
    a177ba5bbd68ad6ada973378c2144635557887b2 Fri Jul 14 12:49:51 2017 -0700
    adding new video and links to it
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5f3ca34a0412ffc6b3e172eb1ca77a72fd5e0e0f Mon Jul 17 10:04:24 2017 -0700
    New version number v352
• src/hg/lib/gtexUi.c
  • lines changed 3, context: html, text, full: html, text
    c4f8088a85119a905e46f1dbaf49e44ec209a792 Tue Jul 11 14:35:31 2017 -0700
    Suppress tisssue selector from popul config, as it's not needed as a tissue legend (unlike GTEx gene track). refs #15646
• src/hg/lib/hgHgvs.c
  • lines changed 11, context: html, text, full: html, text
    2732520d27d9d63e274fd42c0ea225e1a4f35641 Thu Jul 13 13:06:44 2017 -0700
    hgvsToVcfRow was not testing for NULL changeList -- fixed. refs #19702 note-15
• src/hg/makeDb/doc/criGri1.txt
  • lines changed 27, context: html, text, full: html, text
    ed0bf66804ab170c0eab944e32bf970257a9a609 Tue Jul 11 09:59:33 2017 -0700
    add crispr track generation procedure refs #19514
• src/hg/makeDb/doc/hg19.txt
  • lines changed 82, context: html, text, full: html, text
    33af1d6177bcb9cf50b3cf7302f40be4b3583a65 Thu Jul 6 12:43:23 2017 -0700
    Rebuilding hg19 snp150Ortho with latest assemblies from other species; this required running hg19-rheMac8 lastz to get liftOver chains. refs #19202
• src/hg/makeDb/doc/mouseStrains/hubIndex.html
  • lines changed 3, context: html, text, full: html, text
    378652ccedc9588d6b19f5def9b49cab653672c3 Fri Jul 14 12:02:07 2017 -0700
    Editing a sentence as per code review, CR#19768
• src/hg/makeDb/doc/mouseStrains/mouseStrains.html
  • lines changed 73, context: html, text, full: html, text
    4f8a9784b5c9a158752f6d7f5cdca2b1d6a90734 Fri Jul 14 13:14:19 2017 -0700
    Making the html code conform to our HTML guidelines, refs #13553
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    c62e8553ef671c0b94202c7dfd371583170cc13c Fri Jul 14 13:19:29 2017 -0700
    Removing an extra period in the References section, refs #13553
  • lines changed 14, context: html, text, full: html, text
    4ba933cb8963d1662ddac8bb4a9e0f3815df8471 Fri Jul 14 13:33:22 2017 -0700
    Removing extra spaces in the email links and adding Braney's name to the credits, refs #13553
  • lines changed 6, context: html, text, full: html, text
    ef58cd146fe8f409fe51b66375bac64246361440 Fri Jul 14 14:20:28 2017 -0700
    Removing extra spaces in email links, refs #13553
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 26, context: html, text, full: html, text
    12e32063d966167f47e6236fc70d88e9900246cb Wed Jul 12 10:21:22 2017 -0700
    add cpg islands build procedures refs #19777
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh
  • lines changed 1582, context: html, text, full: html, text
    b367f7412b56ee7f5744c7128de5cad1da7e65ac Wed Jul 12 14:37:36 2017 -0700
    Initial commit of mm10 genes v17 doc, refs #19786
• src/hg/makeDb/trackDb/criGri/criGri1/crispr.html
  • lines changed 199, context: html, text, full: html, text
    d41d9ff646a55459dac2ba4a41b8401cd2135159 Fri Jul 14 14:32:34 2017 -0700
    Some criGri1 specific crispr documentation, refs #19514
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    d41d9ff646a55459dac2ba4a41b8401cd2135159 Fri Jul 14 14:32:34 2017 -0700
    Some criGri1 specific crispr documentation, refs #19514
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 2, context: html, text, full: html, text
    f4b6b2643f80431a3b6b23ef3b12ebad53d70f15 Wed Jul 12 11:12:46 2017 -0700
    fixing documentation of crispr track, cutoff is 55, not 60, refs #19782
• src/hg/makeDb/trackDb/human/hg19/crispr.html
  • lines changed 2, context: html, text, full: html, text
    ff36d8a603a5d17411843b41e0573ceb50c6ba1b Wed Jul 12 13:04:01 2017 -0700
    Updating doench 2016 score cutoff for human crispr pages, refs #19514
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    acf4b292102fde92d142fabbb08351163f7d3835 Tue Jul 11 14:44:17 2017 -0700
    Adding in search features for COSMIC tracks, refs #14461
  • lines changed 2, context: html, text, full: html, text
    43bc3bd29bebfedb652da3012186d06428f8d1f9 Tue Jul 11 15:22:29 2017 -0700
    Fixing up trackDb stanzas a bit more, refs #14461
• src/hg/makeDb/trackDb/human/hg38/crispr.html
  • lines changed 2, context: html, text, full: html, text
    ff36d8a603a5d17411843b41e0573ceb50c6ba1b Wed Jul 12 13:04:01 2017 -0700
    Updating doench 2016 score cutoff for human crispr pages, refs #19514
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    acf4b292102fde92d142fabbb08351163f7d3835 Tue Jul 11 14:44:17 2017 -0700
    Adding in search features for COSMIC tracks, refs #14461
  • lines changed 1, context: html, text, full: html, text
    43bc3bd29bebfedb652da3012186d06428f8d1f9 Tue Jul 11 15:22:29 2017 -0700
    Fixing up trackDb stanzas a bit more, refs #14461
• src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
  • lines changed 1, context: html, text, full: html, text
    010ebdcbe24a1e247878a04b00e126d963b21811 Fri Jul 14 13:43:31 2017 -0700
    Fixing a typo, refs #18305
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1bae8bd2805aa58f0560f8a466cc43b2a011b680 Fri Jul 14 11:45:49 2017 -0700
    Removing the release tag for ALL GENCODE VM11 and hiding the previous release by default, refs #19520
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
  • lines changed 1, context: html, text, full: html, text
    1bae8bd2805aa58f0560f8a466cc43b2a011b680 Fri Jul 14 11:45:49 2017 -0700
    Removing the release tag for ALL GENCODE VM11 and hiding the previous release by default, refs #19520
• src/hg/pyLib/hgLib.py
  • lines changed 88, context: html, text, full: html, text
    cf32bd93dfcf0e307c889aaef4e5b1845bbd5a98 Tue Jul 11 17:55:00 2017 -0700
    Adding support for GBIB-style remote /gbdb files to hgGeneGraph. refs #19745
• src/hg/utils/automation/doCrispr.pl
  • lines changed 5, context: html, text, full: html, text
    2b666729ac4d08d038c80a8a6ab7dc8278d30dce Thu Jul 13 17:19:00 2017 -0700
    allow shoulder argument and correct bedClip -truncate and using fasterCrispro.py refs #19514
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    cea77f8093025f6b5c5784b14dc0fd9cbd30f8b3 Fri Jul 14 13:45:36 2017 -0700
    minor fixup in a comment that ends up in the generated scripts refs #19514
• src/inc/obscure.h
  • lines changed 3, context: html, text, full: html, text
    e37af94374417fa6f35f3b8a9a9629226905610a Tue Jul 11 15:31:54 2017 -0700
    would like to have vmPeak value to decide on memory usage refs #18969
• src/lib/obscure.c
  • lines changed 30, context: html, text, full: html, text
    e37af94374417fa6f35f3b8a9a9629226905610a Tue Jul 11 15:31:54 2017 -0700
    would like to have vmPeak value to decide on memory usage refs #18969
• src/utils/bedClip/bedClip.c
  • lines changed 34, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badEnd.result
  • lines changed 5, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badEndExample.bed.gz
  • lines changed 0, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badName.result
  • lines changed 7, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badNameExample.bed.gz
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    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badStart.result
  • lines changed 10, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/badStartExample.bed.gz
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    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/ce6.chrom.sizes
  • lines changed 7, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/clip.result
  • lines changed 10, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/clipExample.bed.gz
  • lines changed 0, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/makefile
  • lines changed 22, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
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    b2bdbec05767ec56a8a070a546959c3da514b354 Tue Jul 11 14:45:02 2017 -0700
    use bedClip binary from PATH refs #19514
• src/utils/bedClip/tests/truncate.result
  • lines changed 12, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/twoFields.result
  • lines changed 5, context: html, text, full: html, text
    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/bedClip/tests/twoFieldsExample.bed.gz
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    b40094812a7c35cef96e0d9b94fa421262947b13 Tue Jul 11 14:43:23 2017 -0700
    adding truncate option and tests to verify everything works refs #19514
• src/utils/crisprKmers/crisprKmers.c
  • lines changed 108, context: html, text, full: html, text
    4a9f5caa2ea145d8ef8d86b6d4abb9a5d70bc345 Tue Jul 11 14:54:48 2017 -0700
    adding score calculation and second PAM sequence refs #18969
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    a6402cd35ac18b36a7d4ee1a6e41df145a519e98 Tue Jul 11 16:03:50 2017 -0700
    prepare to thread this process refs #18969
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    feb770798e0b4ad51ec5b7fc1a82fd1363a66ba1 Wed Jul 12 11:51:53 2017 -0700
    adding threading and eliminate strand char storage, now does not work correctly refs #18969
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    d75dbdc035385f4122259f47091fc09c06ad16c2 Thu Jul 13 11:29:41 2017 -0700
    appears to work OK with threads refs #18969
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    b8456c1e9a533efa1cce9556dd2fd717f83bc7f4 Thu Jul 13 17:13:36 2017 -0700
    get the bed output file open immediately in case there is trouble and do not thread unless explicitly requested refs #18969
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    0f25fca4ed573b955b6a34b8df5c3dcb92331058 Thu Jul 13 18:30:47 2017 -0700
    correct typo refs #18969
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    131be66e554e489d599a2e54988a45f1985e194e Mon Jul 17 08:27:54 2017 -0700
    correct selection of guides vs. ranges to avoid duplicates when ranges are split refs #18969
• src/utils/qa/weeklybld/buildEnv.csh
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    18bfbc2dcae0de9347b04ae04dce6dfce3427c77 Mon Jul 17 10:02:36 2017 -0700
    v352 final build refs #19715

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• files changed: 69