All File Changes

v332_preview2 to v332_base (2016-04-25 to 2016-05-02) v332

• confs/preview.hg.conf
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    7419cb5f58560c6d093e3a0f773370a556d1f1b0 Fri Apr 29 01:11:33 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 4, context: html, text, full: html, text
    75ed2f8276013b7db6206fa33c555dda152607e4 Mon Apr 25 09:09:00 2016 -0700
    hgGateway needs to support position=lastDbPos.
    
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    b7eb0b002d23a4408fdb9d7a3a6520312a889ebc Mon Apr 25 12:53:41 2016 -0700
    Adding back a couple things lost from the original hgGateway (geo mirror check and hub warning check).
    
  • lines changed 34, context: html, text, full: html, text
    485aa503a6d4d83d6aee39332a66e73acac76022 Mon Apr 25 13:29:08 2016 -0700
    Thanks Brian for noticing that the hgwdev warning was missing from the new hgGateway & Cath for suggesting the wording. refs #15277 (notes 192-196).
    
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    f8257545a49d4f3d482e4491f98b5fb5b9d4933a Tue Apr 26 12:29:59 2016 -0700
    Don't show the hgwdev warning box on demo6 so we can use it for screenshots and videos in advance of release (thx Donna and Cath). refs #15277
    
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    c95f690cd307e4d9447cfdeb337c4cc81d21f8aa Wed Apr 27 11:53:56 2016 -0700
    When building list of active genomes and taxIds, join with defaultDb to avoid trouble with same species, different taxId (e.g. species vs. subspecies taxId in sacCer2 vs sacCer3). refs #15277
    
• src/hg/hgGateway/hgGateway.html
  • lines changed 7, context: html, text, full: html, text
    ac78df7079ea1e99ae8426886f2a74099c3418ff Tue Apr 26 09:34:15 2016 -0700
    Position input labeling changes suggested by Cath. refs #15277 (notes 190, 204, 205)
    
  • lines changed 5, context: html, text, full: html, text
    7becab8e9c95f4f90d37ef2f8ea215907534d9b3 Wed Apr 27 17:13:54 2016 -0700
    Fixed problem with 'view sequences' button wrapping down in weird ways when the screen was narrow. refs #15277
    
  • lines changed 1, context: html, text, full: html, text
    8c4510913f781693d99d967eed017e6909e13d4c Thu Apr 28 10:42:01 2016 -0700
    Make sure we support mirrors that don't have all (or any) of our popular species. refs #15277 note 233
    
• src/hg/hgGene/hgGene.c
  • lines changed 3, context: html, text, full: html, text
    f0ffa5ddb60e25932b50b2638100d9fef8e36502 Thu Apr 28 15:07:52 2016 -0700
    highlight the Gencode id on the hgGene page for Gencode.
    
• src/hg/hgSession/hgSession.c
  • lines changed 7, context: html, text, full: html, text
    0e52473a1b54d22035d786d55dcbe130c3604edc Mon Apr 25 16:59:56 2016 -0700
    Jonathan helped overview adding links to hgSession to new Session Gallery page ref #17231
    
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 8, context: html, text, full: html, text
    d48f39fe56017d31ed77b0d389542ada8ff6277a Tue Apr 26 14:07:58 2016 -0700
    Add geneSymbol to the JSON results so it can be used in place of the verbose item value.
    
  • lines changed 6, context: html, text, full: html, text
    21d53b8ef473ed5f371d2dc14ccbbf3303705f2e Thu Apr 28 09:46:26 2016 -0700
    hg38.kgXref has some extremely long descriptions (e.g. CLOCK 4277 chars) that make it difficult to see the actual matching genes in the pop-up menu. Truncate descriptions for autocomplete at 120 chars.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 13, context: html, text, full: html, text
    a52b6ed7d7540d303cbd9edf09ec04f3e818950c Tue Apr 12 17:54:23 2016 -0700
    Add darkerLabels setting.
    
  • lines changed 4, context: html, text, full: html, text
    beb98ce45ec6b8f58d0e5ef448434c57751e8c0c Tue Apr 26 11:04:24 2016 -0700
    fix various problems with BAM coverage mode
    
  • lines changed 1, context: html, text, full: html, text
    c97b4f46cc72547a2a5584bac401bb4b06ef5fae Wed Apr 27 15:58:53 2016 -0700
    Tweak label colors - still readable with less darkening (to stay truer to original)
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    a52b6ed7d7540d303cbd9edf09ec04f3e818950c Tue Apr 12 17:54:23 2016 -0700
    Add darkerLabels setting.
    
  • lines changed 3, context: html, text, full: html, text
    c97b4f46cc72547a2a5584bac401bb4b06ef5fae Wed Apr 27 15:58:53 2016 -0700
    Tweak label colors - still readable with less darkening (to stay truer to original)
    
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    abf17558b1a13e3070d281fea61f39e702a73899 Tue Apr 26 13:51:35 2016 -0700
    adding shortcut for view / reset user settings, refs #17212
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    84f058c937c77736a0f8c72b1dd5e32ef72731fe Mon Apr 25 15:25:54 2016 -0700
    fix a problem with coverage mode in dense
    
  • lines changed 7, context: html, text, full: html, text
    beb98ce45ec6b8f58d0e5ef448434c57751e8c0c Tue Apr 26 11:04:24 2016 -0700
    fix various problems with BAM coverage mode
    
  • lines changed 1, context: html, text, full: html, text
    febf91199af19b2223017f603e55b758d7a1929d Wed Apr 27 09:52:54 2016 -0700
    Correct comment.
    
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    06aae68f351336a5ba55d9c7c5cf0a68607b780f Wed Apr 27 10:16:14 2016 -0700
    Tweak label colors - still readable with less darkening (to stay truer to original)
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 6, context: html, text, full: html, text
    745353d17862d620750bc43032358ba00ea320db Tue Apr 12 13:03:14 2016 -0700
    Show metadata on mouseover of wiggle in full mode when hoverMetadata setting is present. Makes large wiggle composite viewing friendlier. Prompted by 7000 subtrack GTEx signal hub
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    3fbedd09b36991801daaf16fbd55923e565720b6 Tue Apr 26 14:37:20 2016 -0700
    adding rheMac8 release line, fixing to 100 ch limit on credits, refs #17198
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 6, context: html, text, full: html, text
    3fbedd09b36991801daaf16fbd55923e565720b6 Tue Apr 26 14:37:20 2016 -0700
    adding rheMac8 release line, fixing to 100 ch limit on credits, refs #17198
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 31, context: html, text, full: html, text
    16597f50b04d797a692d7b799b8767cdb6fce89a Tue Apr 26 11:14:44 2016 -0700
    Adding links to the Sessions Gallery to Sessions User Guide refs #17231
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 19, context: html, text, full: html, text
    16597f50b04d797a692d7b799b8767cdb6fce89a Tue Apr 26 11:14:44 2016 -0700
    Adding links to the Sessions Gallery to Sessions User Guide refs #17231
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 14, context: html, text, full: html, text
    b41b698689dc47edacdc76d7ccb85d6399f8ebd0 Fri Apr 29 13:17:04 2016 -0700
    Incorporated feedback from paired review, refs #17219. Did some minor editing of Lens PatSeq announcement.
    
  • lines changed 5, context: html, text, full: html, text
    518409b72ca2d03fecf31804ed654a427721d779 Fri Apr 29 13:21:42 2016 -0700
    Added mods made to indexNews.html from paired review, refs #17219.
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    b46a0eac56b1a6700ea6ab8b2383ed76e0b4f330 Thu Apr 28 13:17:04 2016 -0700
    Adding 'Track Search' under 'Genome Browser' menu. refs #15277 notes 227, 229
    
• src/hg/htdocs/indexNews.html
  • lines changed 19, context: html, text, full: html, text
    b41b698689dc47edacdc76d7ccb85d6399f8ebd0 Fri Apr 29 13:17:04 2016 -0700
    Incorporated feedback from paired review, refs #17219. Did some minor editing of Lens PatSeq announcement.
    
• src/hg/htdocs/style/jWest.css
  • lines changed 7, context: html, text, full: html, text
    ac78df7079ea1e99ae8426886f2a74099c3418ff Tue Apr 26 09:34:15 2016 -0700
    Position input labeling changes suggested by Cath. refs #15277 (notes 190, 204, 205)
    
  • lines changed 9, context: html, text, full: html, text
    7becab8e9c95f4f90d37ef2f8ea215907534d9b3 Wed Apr 27 17:13:54 2016 -0700
    Fixed problem with 'view sequences' button wrapping down in weird ways when the screen was narrow. refs #15277
    
• src/hg/inc/versionInfo.h
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    d80445b60cff9e72fcfe51995be767f59a735a36 Mon May 2 10:36:08 2016 -0700
    New version number v332
    
• src/hg/js/hgGateway.js
  • lines changed 33, context: html, text, full: html, text
    773aa9879899908033ea6e64d3344edf069a578e Wed Apr 20 14:47:01 2016 -0700
    Performance improvements: don't do any unnecessary drawing before the first uiState arrives; autocompleteFromTree is actually quite slow so defer it until after the page is displayed.
    
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    ef77b08098f12682c3318243d14dfb52cda203f8 Mon Apr 25 11:50:43 2016 -0700
    Cath's suggestion from #15277#note-190: Use the same width for the select assembly menu as for the position input and center the Go button vertically. Also fixed IE8 clobbering of activeGenomes global. refs #15277
    
  • lines changed 21, context: html, text, full: html, text
    cd093f718a105986a9433d6d99ebd51b6f296805 Mon Apr 25 15:50:51 2016 -0700
    Fix watermark color-switching. refs #15277 (note 149)
    Also add commas to position.
    
  • lines changed 17, context: html, text, full: html, text
    625569a67a2fceb5073d032ab1d26509b82dc694 Tue Apr 26 14:08:28 2016 -0700
    Added logic to keep track of whether the position/search box has a gene selected from autocomplete or something the user typed/pasted in.
    Also added hgsid to the form that sends us to hgTracks -- silly that I was forgetting that!
    refs #15277
    
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    c0c8d67a8b251e347ce93446991664202722c966 Wed Apr 27 11:40:06 2016 -0700
    Scrolling the tree to the selected genome wasn't happening on page load because tree wasn't yet visible -- scroll after .show(). refs #15277
    
  • lines changed 12, context: html, text, full: html, text
    3c89781b651b870cd2c08856116774e3a9a022e7 Wed Apr 27 14:08:38 2016 -0700
    For gene autocomplete, highlight the part of each gene symbol that matches the search term. refs #15277 note 223
    
  • lines changed 5, context: html, text, full: html, text
    7becab8e9c95f4f90d37ef2f8ea215907534d9b3 Wed Apr 27 17:13:54 2016 -0700
    Fixed problem with 'view sequences' button wrapping down in weird ways when the screen was narrow. refs #15277
    
  • lines changed 22, context: html, text, full: html, text
    8c4510913f781693d99d967eed017e6909e13d4c Thu Apr 28 10:42:01 2016 -0700
    Make sure we support mirrors that don't have all (or any) of our popular species. refs #15277 note 233
    
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    b46a0eac56b1a6700ea6ab8b2383ed76e0b4f330 Thu Apr 28 13:17:04 2016 -0700
    Adding 'Track Search' under 'Genome Browser' menu. refs #15277 notes 227, 229
    
• src/hg/lib/genePred.c
  • lines changed 9, context: html, text, full: html, text
    5a54acb02ba08533f895379e2bfd42d0ef779c8e Fri Apr 29 09:45:33 2016 -0700
    improved documentation on CDS issues
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    34875095e36dc30f563d0c3780d4334a2e025be0 Mon Apr 25 14:11:16 2016 -0700
    add additional space before density options in dialog
    
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    beb98ce45ec6b8f58d0e5ef448434c57751e8c0c Tue Apr 26 11:04:24 2016 -0700
    fix various problems with BAM coverage mode
    
  • lines changed 2, context: html, text, full: html, text
    4d748c0d4a31ef6982e0f42f4a26c11f1eb93250 Wed Apr 27 10:31:18 2016 -0700
    fix problem with checkbox in coverage wiggle dialog
    
• src/hg/lib/knownAttrs.as
  • lines changed 16, context: html, text, full: html, text
    f100609c5d2e4a9b54074f4e374972ceb7cefc07 Fri Apr 29 09:30:10 2016 -0700
    add knownAttrs table to capture what's in the wgEncodeGencodeAttrs table
    
• src/hg/lib/knownAttrs.sql
  • lines changed 21, context: html, text, full: html, text
    f100609c5d2e4a9b54074f4e374972ceb7cefc07 Fri Apr 29 09:30:10 2016 -0700
    add knownAttrs table to capture what's in the wgEncodeGencodeAttrs table
    
• src/hg/lib/txGraph.c
  • lines changed 1, context: html, text, full: html, text
    e35f8411576669175e9b0529c0aec04615c0422a Mon May 2 10:28:58 2016 -0700
    changes for Gencode v24 knownGene.
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 151, context: html, text, full: html, text
    e4718f2e9088d9bdec41f57404113a91dbb818d0 Mon Apr 25 13:25:40 2016 -0700
    running up galGal5 and rheMac8 chain net refs #17168 #16744
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 63, context: html, text, full: html, text
    b14549312cebc58411e231b00d62609026abba99 Tue Apr 26 09:50:30 2016 -0700
    adding lastz to galGal5 refs #17168
    
• src/hg/makeDb/doc/oreganno/oreganno.txt
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    32a5f074b018ff6beb83522a6f38cb27a989da45 Thu Apr 28 15:34:07 2016 -0700
    Minor fix to remove extra entries in two tables, refs #15957
    
• src/hg/makeDb/doc/rn6.txt
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    b307a8a5e49149e9e255b38e412f9145ebcda034 Tue Apr 26 15:01:50 2016 -0700
    clone ends done for rn6 refs #16100
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
  • lines changed 104, context: html, text, full: html, text
    6a7bab37f60c67b24fead07c70c27b462a0d9f90 Thu Apr 28 13:21:39 2016 -0700
    some final touchs to hg38 Gencode knownGene before entering into pushq
    
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    f100609c5d2e4a9b54074f4e374972ceb7cefc07 Fri Apr 29 09:30:10 2016 -0700
    add knownAttrs table to capture what's in the wgEncodeGencodeAttrs table
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes16.csh
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    a5b46ebecfb2499d29fa81ebb7bcf33bb839b6da Thu Apr 28 14:21:43 2016 -0700
    Makedoc for latest mm10 UCSC Genes, refs #15315
    
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 11, context: html, text, full: html, text
    e35f8411576669175e9b0529c0aec04615c0422a Mon May 2 10:28:58 2016 -0700
    changes for Gencode v24 knownGene.
    
• src/hg/makeDb/schema/all.joiner
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    ed288ac25bc80ada9ac8e6b9f3dc72826e0e51e1 Tue Apr 26 12:49:52 2016 -0700
    Changing hg38 to hg19 as all of these lift37 all.joiner rules are for hg19, refs #16991
    
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    fe7894675bfc2a92ce87ea2ab4031ea7ff624f00 Tue Apr 26 13:17:45 2016 -0700
    Lowering minCheck for this relationship at markds request, refs #16991
    
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    bb9b1c667a650ececc94f29e1c9a418538f91782 Wed Apr 27 19:18:33 2016 -0700
    all.joiner and trackDb changes for knownGene v24
    
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    18f8bf58de790390e59749d0283d723b915d1305 Thu Apr 28 14:30:13 2016 -0700
    Adding canFam to the list of checked dbs for oregId identifier, refs #15957
    
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    f100609c5d2e4a9b54074f4e374972ceb7cefc07 Fri Apr 29 09:30:10 2016 -0700
    add knownAttrs table to capture what's in the wgEncodeGencodeAttrs table
    
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    c86a10aa728364ba2c9c8d20ad916bbac9992f41 Fri Apr 29 11:17:40 2016 -0700
    Adding cloneEnd tracks to mm10 tablesIgnored, refs #10083
    
• src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
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    4a4dccae5a914cdd6e2288193df51f5d8a4af749 Mon Apr 25 14:08:46 2016 -0700
    updating priorities to inclue galVar1 refs #17180
    
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    9e99d64d56392e795b0dfdcf59c96c042fd296a4 Wed Apr 27 10:12:34 2016 -0700
    chiLan1 is release alpha refs #8476
    
• src/hg/makeDb/trackDb/human/chainNetGalGal5.ra
  • lines changed 15, context: html, text, full: html, text
    6c702285b9ed09c2949e1a2948443b9db619a96d Mon Apr 25 13:30:15 2016 -0700
    adding galGal5 to the composite refs #17168
    
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
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    6c702285b9ed09c2949e1a2948443b9db619a96d Mon Apr 25 13:30:15 2016 -0700
    adding galGal5 to the composite refs #17168
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    23e45dee2d3256c27bd6a3851fdf37b5dfebcbb8 Tue Apr 26 16:16:40 2016 -0700
    Removing sections from ra file and description page for 2-way and poly-A tracks as they are not part of this release. Add this new release to track description pages. refs #16991
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.html
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    23e45dee2d3256c27bd6a3851fdf37b5dfebcbb8 Tue Apr 26 16:16:40 2016 -0700
    Removing sections from ra file and description page for 2-way and poly-A tracks as they are not part of this release. Add this new release to track description pages. refs #16991
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.ra
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    23e45dee2d3256c27bd6a3851fdf37b5dfebcbb8 Tue Apr 26 16:16:40 2016 -0700
    Removing sections from ra file and description page for 2-way and poly-A tracks as they are not part of this release. Add this new release to track description pages. refs #16991
    
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    6c2a52a6839a66ea22dc531d5ce3e3a8c3619b4e Fri Apr 29 12:52:20 2016 -0700
    V24lift37 doesn't have exon supports table, remove it from trackDb
    
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    9ae6bb66619808b5e526f85391072e3543a8b671 Mon May 2 09:33:02 2016 -0700
    Hiding V24lift37 by default at markds recommendation, as this is a remapping not an official release, refs #16991
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    bb9b1c667a650ececc94f29e1c9a418538f91782 Wed Apr 27 19:18:33 2016 -0700
    all.joiner and trackDb changes for knownGene v24
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    bb9b1c667a650ececc94f29e1c9a418538f91782 Wed Apr 27 19:18:33 2016 -0700
    all.joiner and trackDb changes for knownGene v24
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    bb9b1c667a650ececc94f29e1c9a418538f91782 Wed Apr 27 19:18:33 2016 -0700
    all.joiner and trackDb changes for knownGene v24
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    a5d55b6885daf7001999b267c2574c838ec93d5d Mon Apr 25 12:04:34 2016 -0700
    Add trackDb setting to change label colors on a track to a slightly darker shade for better visibility. Useful when there are many subtracks, and/or colors are externally defined
    
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    acf102426f7bab55a2c7fa93de6b7af01cba8827 Mon Apr 25 12:49:08 2016 -0700
    Add search for other sites to link back to GTEx gene.
    
• src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra
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    8382074ff1514611ee3f9e296e9d425107940abb Fri Apr 29 12:05:02 2016 -0700
    Fixing short label lengths, refs #10083
    
• src/hg/makeDb/trackDb/mouse/mm10/chainNetGalGal4.ra
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    7ea02787d82801bc74a30f9069b3da61ea923217 Mon Apr 25 13:48:39 2016 -0700
    adding galGal5 to the alpha composite refs #17168
    
• src/hg/makeDb/trackDb/mouse/mm10/chainNetGalGal5.ra
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    7ea02787d82801bc74a30f9069b3da61ea923217 Mon Apr 25 13:48:39 2016 -0700
    adding galGal5 to the alpha composite refs #17168
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
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    7ea02787d82801bc74a30f9069b3da61ea923217 Mon Apr 25 13:48:39 2016 -0700
    adding galGal5 to the alpha composite refs #17168
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    7ea02787d82801bc74a30f9069b3da61ea923217 Mon Apr 25 13:48:39 2016 -0700
    adding galGal5 to the alpha composite refs #17168
    
• src/hg/makeDb/trackDb/rat/rn6/cloneEnd.trackDb.ra
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    b2f9f3ae77ac5e64a822b4d8bc8f0f4919880e70 Tue Apr 26 14:55:09 2016 -0700
    adding clone ends for rn6 refs #16100
    
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    57d5e44e1dac1d990cbdb135f7c168f4da2f208e Wed Apr 27 10:44:39 2016 -0700
    fixup the name search rules for the cloneEndbadEnds and cloneEndmultipleMaps tables refs #16100
    
• src/hg/makeDb/trackDb/rat/rn6/cloneEndSuper.html
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    b2f9f3ae77ac5e64a822b4d8bc8f0f4919880e70 Tue Apr 26 14:55:09 2016 -0700
    adding clone ends for rn6 refs #16100
    
• src/hg/makeDb/trackDb/rat/rn6/trackDb.ra
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    b2f9f3ae77ac5e64a822b4d8bc8f0f4919880e70 Tue Apr 26 14:55:09 2016 -0700
    adding clone ends for rn6 refs #16100
    
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
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    4e899c28f579e4bb0104bac4baa4502da1c13ef9 Fri Apr 29 11:06:18 2016 -0700
    Adding pennant icons for saccer2,3 oreganno, refs #15957
    
• src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
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    4e899c28f579e4bb0104bac4baa4502da1c13ef9 Fri Apr 29 11:06:18 2016 -0700
    Adding pennant icons for saccer2,3 oreganno, refs #15957
    
• src/hg/makeDb/trackDb/tagTypes.tab
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    a5d55b6885daf7001999b267c2574c838ec93d5d Mon Apr 25 12:04:34 2016 -0700
    Add trackDb setting to change label colors on a track to a slightly darker shade for better visibility. Useful when there are many subtracks, and/or colors are externally defined
    
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    e173eef8a4f1c26aff803b7f79cdac0fe560f8dc Tue Apr 26 16:39:29 2016 -0700
    Remove temp setting.
    
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    3761e305ef65c73d8b873737a4b5d6dde101974c Tue Apr 26 16:41:48 2016 -0700
    Add setting to show metadata line on mouse hover over a wiggle (full mode). We might want to make this default, but for now turn on with this setting.
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    fb7ba09d6f758ef839822e3619fb8a6e3c1aa367 Mon Apr 25 12:36:18 2016 -0700
    adding galGal5 for hg38 refs #17168
    
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    f076731a2fae342435567d7ac3dc2996e3e2879b Wed Apr 27 10:06:39 2016 -0700
    adding galVar1 chain net definitions refs #17180
    
• src/hg/txGraph/txgAnalyze/txgAnalyze.c
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    e35f8411576669175e9b0529c0aec04615c0422a Mon May 2 10:28:58 2016 -0700
    changes for Gencode v24 knownGene.
    
• src/hg/utils/automation/doIdKeys.pl
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    d4b065a0d16c08fb851cffb465a3d9d979631cc4 Thu Apr 28 13:53:17 2016 -0700
    ready to run the cluster run refs #17168
    
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    5b5f04b6df27df6b5a12bf3dbd9d87b70f1c8d29 Thu Apr 28 15:05:42 2016 -0700
    completed through cleanup step refs #17168
    
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    2af610eac42f5daca0563c64823c5a8fc33ea0db Thu Apr 28 15:22:52 2016 -0700
    correct identification of duplicate message from twoBitDup refs #17168
    
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    eb792621f50a815e228ec6bfeea743cc2aa791e4 Thu Apr 28 15:34:46 2016 -0700
    correct parts.list name refs #17168
    
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    6232279cf24d7032a5e2e87776f8ec9146e2fca5 Mon May 2 10:27:15 2016 -0700
    adding dup status check refs #17168
    
• src/hg/utils/automation/makefile
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    84aca9ec4f47c29866c97ecca57acd0ccbf6eae1 Thu Apr 28 15:07:08 2016 -0700
    adding doIdKeys.pl to the utils list refs #17168
    
• src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
    fixed bug with merger negative strand gaps due to incorrect frame test
    
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    48c9b138b777d310591c9a4e0b3efdd768b9679d Tue Apr 26 19:11:47 2016 -0700
    fixed a bug with frame when gap filling on reverse strand
    
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
    added new test cases
    
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
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    48c9b138b777d310591c9a4e0b3efdd768b9679d Tue Apr 26 19:11:47 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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    48c9b138b777d310591c9a4e0b3efdd768b9679d Tue Apr 26 19:11:47 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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• src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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• src/hg/utils/transMapPslToGenePred/tests/makefile
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
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    48c9b138b777d310591c9a4e0b3efdd768b9679d Tue Apr 26 19:11:47 2016 -0700
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• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    f3406d68a298ea5b567b5d67bc05db6ecabc3b92 Tue Apr 26 12:29:03 2016 -0700
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    885abd78d6f56c4dbca20603d976491d3cfceddf Fri Apr 29 09:56:32 2016 -0700
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• src/utils/qa/weeklybld/buildEnv.csh
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    acb438cacab3a891d74f5c5f4dc23917dfda4ebb Mon May 2 10:34:57 2016 -0700
    v332 final build refs #17202
    
• src/utils/qa/weeklybld/doNewBranch.csh
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    8e274b8cb5a133c2bd0a8ce1beee06ff02b2a4fd Mon Apr 25 10:55:56 2016 -0700
    temporary change of email address while Ann is out refs #17202
    
• src/utils/qa/weeklybld/doNewReview.csh
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    8e274b8cb5a133c2bd0a8ce1beee06ff02b2a4fd Mon Apr 25 10:55:56 2016 -0700
    temporary change of email address while Ann is out refs #17202
    
• src/utils/qa/weeklybld/doNewReview2.csh
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• src/utils/qa/weeklybld/sendLogEmail.pl
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    temporary change of email address while Ann is out refs #17202
    
• src/utils/twoBitDup/twoBitDup.c
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    2a7d8d36d651b483f7624b95c494086d5595ebf5 Mon Apr 25 10:20:41 2016 -0700
    hashVal is not unique for different strings, try using md5sum refs #17168
    
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    9217651e6774e9963587e76f203bac2df8b7a81e Thu Apr 28 15:21:10 2016 -0700
    ready to use with doIdKeys.pl automation script refs #17168
    

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