All File Changes

v301_preview to v301_preview2 (2014-05-26 to 2014-06-02) v301

• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit
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    Bug 1481 Rephrase submission email message per Brian's note 12
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    remove the edwSubmit binary from git
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 11, context: html, text, full: html, text
    Bug 1481 Rephrase submission email message per Brian's note 12
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 61, context: html, text, full: html, text
    encode bug 1481edwWebSubmit issue when multiple URL/users submit same validated.txt
    
  • lines changed 7, context: html, text, full: html, text
    Bug 1481 Rephrase submission display per Brian's note 12
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c
  • lines changed 54, context: html, text, full: html, text
    Librarified fq i/o
• src/hg/genePredToBed/genePredToBed.c
  • lines changed 6, context: html, text, full: html, text
    fixing CDS problem in genePredToBed
  • lines changed 6, context: html, text, full: html, text
    taking back two changes from earlier today to genePredToBed.c and bed.cafter I realized (and reminded by Braney) that the problem was entirely
    different.
    
• src/hg/hgGateway/hgGateway.c
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    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    some code clean-ups in response to code review
  • lines changed 9, context: html, text, full: html, text
    some small fixes for hub search ui
  • lines changed 4, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
  • lines changed 19, context: html, text, full: html, text
    change the linkouts on hgHubConnect to pointt to hub.txt for shortLabeland to descriptionUrl for longLabel
    
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/hgTracks/encode.c
  • lines changed 1, context: html, text, full: html, text
    Show ENCODE peaks full height if no peak summit is shown. refs #13305
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/hgTracks/multiWig.c
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    add Watson Cricket mode
• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    Accidentally removed pgSnp tracks' dense mode left labels in a430d3db1;adding them back now.
    refs #13220, fixes #13344
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    fix border case in snake drawing that Dent and Ben found
• src/hg/hgTracks/wigCommon.h
  • lines changed 3, context: html, text, full: html, text
    add Watson Cricket mode
• src/hg/hgTracks/wigTrack.c
  • lines changed 12, context: html, text, full: html, text
    add Watson Cricket mode
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/hgc/hgc.c
  • lines changed 30, context: html, text, full: html, text
    Add mapping of ids to names for extra fields. Reusing the extra fields code instead of adding track-specific code. refs #13230
  • lines changed 51, context: html, text, full: html, text
    Cleanup to isolate id/name mapping code. refs #13230
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    adding note about thickStart/thickEnd to BED FAQ
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 10, context: html, text, full: html, text
    Adding note about auto updates being slow on DSL lines, recommend turning them off. Fixing up note about ways to potentially fix a broken GBiB, refs #12843
  • lines changed 2, context: html, text, full: html, text
    removed mention of auto-update interval. refs #12843
• src/hg/htdocs/goldenPath/help/hgQuickStartHub.html
  • lines changed 6, context: html, text, full: html, text
    Code review changes refs #13329
  • lines changed 331, context: html, text, full: html, text
    Renaming file following code review suggestions #13251
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    Adding link to new hub Quick Start Guide refs #6753
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 331, context: html, text, full: html, text
    Renaming file following code review suggestions #13251
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 41, context: html, text, full: html, text
    adding announcement for new Roadmap hub, refs #13023
  • lines changed 23, context: html, text, full: html, text
    Adding announcement for EVS Variants track. Removed UCSC Gene and 3 assembly announcements. refs #9329
• src/hg/htdocs/indexNews.html
  • lines changed 89, context: html, text, full: html, text
    adding announcement for new Roadmap hub, refs #13023
  • lines changed 149, context: html, text, full: html, text
    Adding announcement for EVS Variants track. Removed UCSC Gene and 3 assembly announcements. refs #9329
• src/hg/inc/bed5Sources.h
  • lines changed 82, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 82, context: html, text, full: html, text
    Removing unneeded file schema code. refs #13230
• src/hg/inc/hubConnect.h
  • lines changed 1, context: html, text, full: html, text
    some code clean-ups in response to code review
  • lines changed 13, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/inc/wiggle.h
  • lines changed 6, context: html, text, full: html, text
    add Watson Cricket mode
• src/hg/js/hgHubConnect.js
  • lines changed 6, context: html, text, full: html, text
    some small fixes for hub search ui
• src/hg/lib/bed.c
  • lines changed 7, context: html, text, full: html, text
    fixing another gp->bed converter used byhg/altSplice/altSplice/genePredToBed.c, but not by
    hg/genePredToBed/genePredToBed.c
    
  • lines changed 7, context: html, text, full: html, text
    taking back two changes from earlier today to genePredToBed.c and bed.cafter I realized (and reminded by Braney) that the problem was entirely
    different.
    
• src/hg/lib/bed5Sources.as
  • lines changed 12, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 3, context: html, text, full: html, text
    Trim field name for hgc extraFields cosmetics
• src/hg/lib/bed5Sources.c
  • lines changed 208, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 208, context: html, text, full: html, text
    Removing unneeded file schema code. refs #13230
• src/hg/lib/bed5Sources.sql
  • lines changed 19, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    some code clean-ups in response to code review
  • lines changed 10, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/lib/hubConnect.c
  • lines changed 37, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    add Watson Cricket mode
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 1, context: html, text, full: html, text
    Removing unneeded file schema code. refs #13230
• src/hg/lib/trackHub.c
  • lines changed 40, context: html, text, full: html, text
    clean up some code for opening trackHubs, removed hgHubConnectCgiDestUrlcart variable, added ability to tell CGI's to default to a particular
    database supported by a hub
    
• src/hg/lib/wgEncodeAwgDnaseCombinedSources.as
  • lines changed 6, context: html, text, full: html, text
    Adding as file for source name table
  • lines changed 3, context: html, text, full: html, text
    Fix up schema for tableDescriptions
• src/hg/lib/wiggleCart.c
  • lines changed 12, context: html, text, full: html, text
    add Watson Cricket mode
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 15, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 35, context: html, text, full: html, text
    Minor doc changes
  • lines changed 31, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 1, context: html, text, full: html, text
    Updating make doc.
• src/hg/makeDb/doc/fr1.txt
  • lines changed 27, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/galGal2.txt
  • lines changed 28, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/hg16.txt
  • lines changed 26, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/hg19.txt
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    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/hg/makeDb/doc/hg38.txt
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    adding panTro4 and monDom5 lastz chain net refs #13300
  • lines changed 30, context: html, text, full: html, text
    adding panTro4 and monDom5 lastz chain net refs #13300
  • lines changed 48, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
  • lines changed 2, context: html, text, full: html, text
    correct directory name for cytoBand refs #11681
• src/hg/makeDb/doc/mm10.txt
  • lines changed 12, context: html, text, full: html, text
    run up rheMac2 mm10 liftOver per user request refs #13319
• src/hg/makeDb/doc/mm9.txt
  • lines changed 16, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 8, context: html, text, full: html, text
    lift over to ochPri3 refs #9347
• src/hg/makeDb/doc/panTro1.txt
  • lines changed 27, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/rn3.txt
  • lines changed 33, context: html, text, full: html, text
    unmasked CpG island track contruction refs #1268
• src/hg/makeDb/doc/rn5.txt
  • lines changed 3, context: html, text, full: html, text
    Adding final bits to rn5 multiz13way. refs #8212
• src/hg/makeDb/hgBedSources/hgBedSources.c
  • lines changed 138, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
• src/hg/makeDb/hgBedSources/makefile
  • lines changed 3, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
• src/hg/makeDb/hgBedSources/test.in.bed
  • lines changed 10, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
• src/hg/makeDb/hgBedSources/test.out.bed
  • lines changed 10, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
• src/hg/makeDb/trackDb/apis/apiMel2/brhInparalog.html
  • lines changed 1, context: html, text, full: html, text
    updating UniRef50 link per code review, refs #13289
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 17, context: html, text, full: html, text
    adding in Arctic lamprey letCam1 refs #13300
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
  • lines changed 16, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 5, context: html, text, full: html, text
    Add settings to display ids as cell types with links. refs #13230
  • lines changed 1, context: html, text, full: html, text
    Label tweak for consistency.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseCombinedSites.html
  • lines changed 60, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 56, context: html, text, full: html, text
    Refine track description. refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMaster.html
  • lines changed 60, context: html, text, full: html, text
    Draft track description using text from Chromatin landscapes paper. refs #13230
• src/hg/makeDb/trackDb/human/hg38/omimDescriptionText.html
  • lines changed 52, context: html, text, full: html, text
    Added comment for hg38 OMIM tracks that dbSNP is not available, which limits it a bit. These files (omimDescriptionText.html, omimGene2.html, omimLocation.html) to be removed from the hg38/ directory after dbSnp is added and confirmed to work with this track.
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 77, context: html, text, full: html, text
    Added comment for hg38 OMIM tracks that dbSNP is not available, which limits it a bit. These files (omimDescriptionText.html, omimGene2.html, omimLocation.html) to be removed from the hg38/ directory after dbSnp is added and confirmed to work with this track.
• src/hg/makeDb/trackDb/human/hg38/omimLocation.html
  • lines changed 71, context: html, text, full: html, text
    Added comment for hg38 OMIM tracks that dbSNP is not available, which limits it a bit. These files (omimDescriptionText.html, omimGene2.html, omimLocation.html) to be removed from the hg38/ directory after dbSnp is added and confirmed to work with this track.
• src/hg/makeDb/trackDb/human/lrg.html
  • lines changed 8, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/hg/makeDb/trackDb/human/lrgTranscriptAli.html
  • lines changed 8, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 4, context: html, text, full: html, text
    More minor edits to description page to make it specific to the 13-way refs #8212
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    DNase Combined track from ENCODE Analysis, with new data format (BED5Sources). Similar to factorSource, but more general and lighter-weight. refs #13230.
  • lines changed 2, context: html, text, full: html, text
    Add settings to display ids as cell types with links. refs #13230
• src/hg/makeDb/trackDb/trackDb.chainNet.afrotheria.ra
  • lines changed 176, context: html, text, full: html, text
    catching up chain net tracks refs #13300
  • lines changed 118, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
• src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra
  • lines changed 530, context: html, text, full: html, text
    catching up with chain net definitions refs #13300
  • lines changed 126, context: html, text, full: html, text
    catching up chain net tracks refs #13300
• src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra
  • lines changed 353, context: html, text, full: html, text
    catching up chain net tracks refs #13300
• src/hg/makeDb/trackDb/trackDb.chainNet.fish.ra
  • lines changed 471, context: html, text, full: html, text
    catching up chain net tracks refs #13300
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
  • lines changed 884, context: html, text, full: html, text
    catching up chain net tracks refs #13300
  • lines changed 59, context: html, text, full: html, text
    adding chlSab1 - Green monkey - Chlorocebus sabaeus and phyCat1 - Sperm whale - Physeter catodon refs #13300
  • lines changed 177, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
  • lines changed 59, context: html, text, full: html, text
    adding eriEur2 chain net refs #10272
• src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
  • lines changed 176, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
  • lines changed 176, context: html, text, full: html, text
    catching up with chain net definitions refs #13300
  • lines changed 59, context: html, text, full: html, text
    catching up chain net tracks refs #13300
  • lines changed 59, context: html, text, full: html, text
    adding chlSab1 - Green monkey - Chlorocebus sabaeus and phyCat1 - Sperm whale - Physeter catodon refs #13300
  • lines changed 59, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
• src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
  • lines changed 353, context: html, text, full: html, text
    catching up chain net tracks refs #13300
  • lines changed 118, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    catching up chain net tracks refs #13300
  • lines changed 14, context: html, text, full: html, text
    Removing stanza for cpgIslandExt track because it is now part of the cpgIslandSuper super track, refs #13268
  • lines changed 3, context: html, text, full: html, text
    Removing release tags for cpgIslandSuper track and subtracks, refs #13268
  • lines changed 7, context: html, text, full: html, text
    Trying out a new search rule for farm animal QTL track. refs #10954
  • lines changed 1, context: html, text, full: html, text
    catching up chain net track definitions refs #10272
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Defining UNAME_S per Hiram's feedback, since it is not like I assume defined already.
• src/hg/oneShot/tryGtexBoxPlot/makefile
  • lines changed 3, context: html, text, full: html, text
    First cut at a GTEx fake plotter
• src/hg/oneShot/tryGtexBoxPlot/tryGtexBoxPlot.c
  • lines changed 218, context: html, text, full: html, text
    First cut at a GTEx fake plotter
  • lines changed 122, context: html, text, full: html, text
    It's doing a passible imitation of a Tukey box plot.
  • lines changed 12, context: html, text, full: html, text
    Making outliers dots only appear outside of whiskers.
• src/hg/pslToBed/pslToBed.c
  • lines changed 2, context: html, text, full: html, text
    changes after code review, refs #13332
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 3, context: html, text, full: html, text
    correctly md5sum the syntenic net downloads refs #13300
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 31, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/hg/utils/phyloTrees/130way.dissect.txt
  • lines changed 1813, context: html, text, full: html, text
    raising the bar to 130 species refs #10272
• src/hg/utils/phyloTrees/130wayChainNet.pl
  • lines changed 212, context: html, text, full: html, text
    raising the bar to 130 species refs #10272
• src/hg/utils/phyloTrees/131way.commonNames.nh
  • lines changed 131, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/131way.dissect.txt
  • lines changed 1827, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/131way.nh
  • lines changed 131, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/131way.scientificNames.nh
  • lines changed 131, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/131wayChainNet.pl
  • lines changed 212, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/findScores.pl
  • lines changed 1, context: html, text, full: html, text
    correctly parsing new style Q matrix settings refs #13300
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding sperm whale refs #10272
• src/inc/fq.h
  • lines changed 15, context: html, text, full: html, text
    Librarified fq i/o
• src/lib/README
  • lines changed 10, context: html, text, full: html, text
    happened to stumble over this: patent notice not necessary anymore since2004.
    
• src/lib/annoStreamVcf.c
  • lines changed 12, context: html, text, full: html, text
    When position was set to a chrom not present in a VCF+tabix file,annoStreamVcf just kept reading rows out of the file instead of
    paying attention to the return value of lineFileSetTabixRegion.
    This inefficiency led to carefulMem running into its 6G limit.
    Fix: if lineFileSetTabixRegion fails in asvSetRegion, set self->eof
    to prevent reading out rows from the wrong position. If we're trying
    to skip ahead to minChrom using lineFileSetTabixRegion in
    nextRowUnfiltered, and it fails, just keep current position in case
    the file has more chroms after minChrom.
    fixes #13343
    
• src/lib/axt.c
  • lines changed 3, context: html, text, full: html, text
    Adding a few UC Regents Copyrights I missed in last round.
• src/lib/common.c
  • lines changed 31, context: html, text, full: html, text
    Polishing doubleBoxWhiskerCalc to work well for small Ns.
• src/lib/diGraph.c
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    Adding Jim Kent copyright notices to a few files that needed it.
• src/lib/filePath.c
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    Adding a few UC Regents Copyrights I missed in last round.
• src/lib/flydna.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/fof.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/fq.c
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    Librarified fq i/o
• src/lib/gff.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/gfxPoly.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/maf.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/mafFromAxt.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/makefile
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    Librarified fq i/o
• src/lib/mgCircle.c
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    Adding Jim Kent copyright notices to a few files that needed it.
• src/lib/mgPolygon.c
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    Adding Jim Kent copyright notices to a few files that needed it.
• src/lib/pipeline.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/psGfx.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/psPoly.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/pslTbl.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/rainbow.c
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    Adding Jim Kent copyright notices to a few files that needed it.
• src/lib/scoreWindow.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/seg.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/xAli.c
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    Adding Jim Kent copyright notices to a few files that needed it.
• src/lib/xa.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/lib/xenshow.c
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    Adding spacing for readability around some copyrights notices that needed it.
• src/test/buildTableDescriptions.pl
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    Adding header comment
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    Remove debug stuff
• src/utils/qa/bamToBigWig.csh
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    added 54844 to chromsizes file as suggested by Jonathan. Refs #13331
• src/utils/qa/weeklybld/buildEnv.csh
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    v301 preview2 refs #13189

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