All File Changes

v302_preview to v302_preview2 (2014-06-16 to 2014-06-23) v302

• src/hg/hgHubConnect/hgHubConnect.c
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    add a couple features requested in #11633
• src/hg/hgTracks/chromGraphTrack.c
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    Fixes #13440. Make chromGraph track height for dense immitate simple bed track height initialization.
• src/hg/hgc/hgc.c
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    Angie caught my bug in code review. Thanks! #13457.
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
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    add some text for "negate values"
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    some text for negateValues in wiggle help, and in trackDb settings
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    Removing word from sentence to make it sound better, mentioned by Jonathan in code review a few weeks ago, refs #13241
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    some text for negateValues in wiggle help, and in trackDb settings
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
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    some text for negateValues in wiggle help, and in trackDb settings
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    some text for negateValues in wiggle help, and in trackDb settings
• src/hg/htdocs/goldenPath/newsarch.html
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    Added links to Raney et al. track hubs doc (in case a user decides to look for it in the news archives).
  • lines changed 32, context: html, text, full: html, text
    adding announcement for rn5 conservation track, refs #8212
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    Changing a few lines of rn5 conservation track announcement based on feedback, refs #8212
• src/hg/htdocs/goldenPath/pubs.html
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    Added pub on Ragout, per Brian Raney.
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    Added mdash to Ragout citation.
• src/hg/htdocs/indexIntro.html
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    Changed some formatting of donation button, added some explanatory text for it and made a few edits to existing intro text.
• src/hg/htdocs/indexNews.html
  • lines changed 80, context: html, text, full: html, text
    adding announcement for rn5 conservation track, refs #8212
  • lines changed 6, context: html, text, full: html, text
    Changing a few lines of rn5 conservation track announcement based on feedback, refs #8212
• src/hg/inc/bigBedFind.h
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    enable bigBed item search on native bigBed tracks
• src/hg/inc/hdb.h
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    hdb's hGetParent wasn't working because it used hMaybeTrackInfo whichlooks up only one track, not its parent or children. It was used in only
    one place in the code, so I replaced it with a call to tdbForTrack.
    fixes #13477 (Search results don't open super tracks)
    
• src/hg/inc/trackHub.h
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    some slightly better error handling on hub connects
• src/hg/js/makefile
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    In code review I noticed two files that were defined as both JQUERY_UNTOUCHED and JQUERY_MODIFIED. Both belong only on MODIFIED list.
• src/hg/lib/bigBedFind.c
  • lines changed 143, context: html, text, full: html, text
    enable bigBed item search on native bigBed tracks
  • lines changed 9, context: html, text, full: html, text
    fix a bug that Angie found in bigBed track item search
• src/hg/lib/googleAnalytics.c
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    updated to Universal Analytics code refs #13120
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    add display features to get demographics refs #13120
• src/hg/lib/hdb.c
  • lines changed 22, context: html, text, full: html, text
    hdb's hGetParent wasn't working because it used hMaybeTrackInfo whichlooks up only one track, not its parent or children. It was used in only
    one place in the code, so I replaced it with a call to tdbForTrack.
    fixes #13477 (Search results don't open super tracks)
    
• src/hg/lib/hgFind.c
  • lines changed 14, context: html, text, full: html, text
    enable bigBed item search on native bigBed tracks
  • lines changed 17, context: html, text, full: html, text
    hdb's hGetParent wasn't working because it used hMaybeTrackInfo whichlooks up only one track, not its parent or children. It was used in only
    one place in the code, so I replaced it with a call to tdbForTrack.
    fixes #13477 (Search results don't open super tracks)
    
  • lines changed 4, context: html, text, full: html, text
    fix a bug that Angie found in bigBed track item search
• src/hg/lib/hubConnect.c
  • lines changed 8, context: html, text, full: html, text
    some slightly better error handling on hub connects
• src/hg/lib/hui.c
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    don't check min and max on y lines in wiggles.
• src/hg/lib/makefile
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    enable bigBed item search on native bigBed tracks
• src/hg/lib/trackHub.c
  • lines changed 125, context: html, text, full: html, text
    enable bigBed item search on native bigBed tracks
  • lines changed 8, context: html, text, full: html, text
    add a couple features requested in #11633
• src/hg/makeDb/doc/dm6.txt
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    GB Track #13461 Conservation Track for dm6Finished LASTZ chain/net dm6 with
    group one: 9 assemblies used by dm3
    D. ananassae Feb. 2006 (droAna3)
    D. erecta Feb. 2006 (droEre2)
    D. grimshawi Feb. 2006 (droGri2)
    D. persimilis Oct. 2005 (droPer1)
    D. simulans Apr. 2005 (droSim1)
    D. sechellia Oct. 2005 (droSec1)
    D. virilis Feb. 2006 (droVir3)
    A. gambiae Feb. 2003 (anoGam1)
    T. castaneum Sep. 2005 (triCas2)
    
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    Flag sections skipped
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    Track #13461 Conservation Track for dm6Add LASTZ chain/net from dm6 to
    droPse3 46245 D. pseudoobscura 11 Apr 2013 (Dpse_3.0/droPse3)
    droWil2 7260 D. willistoni 03 Aug 2006 (dwil_caf1/droWil2)
    droYak3 7245 D. yakuba 27 Jun 2006 (dyak_caf1/droYak3)
    apiMel4 7460 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4)
    
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    Track #13461 Conservation Track for dm6Finished LASTZ chain/net for
    dp4
    Drosophila_pseudoobscura
    Drosophila_willistoni
    Drosophila_yakuba
    Apis_mellifera
    Drosophila_albomicans
    Drosophila_biarmipes
    Drosophila_bipectinata
    Drosophila_elegans
    Drosophila_eugracilis
    Drosophila_ficusphila
    Drosophila_kikkawai
    Drosophila_miranda
    Drosophila_rhopaloa
    Drosophila_suzukii
    Drosophila_takahashii
    Musca_domestic
    
• src/hg/makeDb/doc/quickAssembly.txt
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    adding insect procedure refs #13461
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    recording timings in the log files refs #252
• src/hg/makeDb/trackDb/animalQtl.html
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    Minor edit to farm animal QTL description pg. refs #10954
• src/hg/makeDb/trackDb/grcIncidentDb.html
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    eliminate human specific comments, this is genric refs #13459
• src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra
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    User suggestion - make lincRNAsTranscripts searchable.refs #13475
    
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    Tweak to lincRNAsTranscripts search: all but one name in this trackare TCONS_* accessions that should short-circuit. The one anomalous
    name is a gene name and should not short-circuit, so it will go on
    to get matches in gene and genbank tracks.
    
• src/hg/makeDb/trackDb/lamprey/petMar2/lampreyGene.html
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    made changes per code review #13452
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
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    default pack for chainNetHg19 refs #9347
• src/hg/makeDb/trackDb/rat/rn5/cons13way.ra
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    Turning some species off by default for rn5 13way. refs #8212
• src/hg/makeDb/trackDb/tagTypes.tab
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    enable bigBed item search on native bigBed tracks
• src/hg/makeDb/trackDb/trackDb.ra
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    Removed semiShortCircuit behavior from stsMapAliasMrnaAcc becausesome aliases conflict with gene names, and if it triggers a short
    circuit then the user never sees the matches in gene & genbank tracks.
    
• src/hg/utils/phyloTrees/145way.nh
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    continue adding to tree refs #10272
• src/hg/utils/phyloTrees/150way.nh
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    up to 150 species perhaps 16 more to come immediately refs #10272
• src/hg/utils/phyloTrees/166way.commonNames.nh
  • lines changed 166, context: html, text, full: html, text
    catching up common and scientific names refs #10272
• src/hg/utils/phyloTrees/166way.nh
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    up to date with released genomes available 13 June 2014 refs ##10272
• src/hg/utils/phyloTrees/166way.scientificNames.nh
  • lines changed 166, context: html, text, full: html, text
    catching up common and scientific names refs #10272
• src/hg/utils/phyloTrees/db.ncbiTaxId.tab
  • lines changed 171, context: html, text, full: html, text
    adding in invertebrates refs #4049
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    adding five new birds refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 22, context: html, text, full: html, text
    adding the Drosophila group refs #13461
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    adding house fly musDom2 refs #13461
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    catching up common and scientific names refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    catching up common and scientific names refs #10272
• src/lib/annoStreamVcf.c
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    In asvSetRegion, don't try to set tabix region if chrom is NULL (position is genome)because that call will fail and then we'd get the wrong idea and set self->eof, oops.
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v302 preview2 refs #13448
• src/weblet/bottleneck/bottleneck.c
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    Fixed typo preventing the port option from working

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• files changed: 63