All File Changes

v308_base to v309_preview (2014-11-03 to 2014-11-10) v309

• src/hg/autoSql/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/embossToPsl/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/estOrient/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/gbGetEntries/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/genePredHisto/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/genePredSingleCover/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/genePredToGtf/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/genePredToMafFrames/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/hgConvert/hgConvert.c
  • lines changed 1, context: html, text, full: html, text
    fixing bug where hgLiftOver would not map regions on the gbib. Also adding a progress message so the user has some idea what's going on.
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 7, context: html, text, full: html, text
    add linkout from hgGene to GENCODE #14904
• src/hg/hgGetAnn/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 2, context: html, text, full: html, text
    change "This hub not supported" message #14133
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    removed duplicated line in last gbib commit (e30e926564), refs #14176
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    Registering track handlers for snp142 tracks.refs #14189
    
• src/hg/hgc/hgc.c
  • lines changed 6, context: html, text, full: html, text
    Better display of allele count total for SNPs tracks -- before I wasextrapolating total2N from frequency but that isn't precise enough for
    very low frequencies.
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 12, context: html, text, full: html, text
    adding links to blogs and video
• src/hg/htdocs/indexIntro.html
  • lines changed 7, context: html, text, full: html, text
    adding link to store to top section of home page
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    add "hubClear" url variable to tell the browser to connect theassociated hub, and to disconnect from all the hubs with the same
    prefix. #13382
    
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    fixing bug where hgLiftOver would not map regions on the gbib. Also adding a progress message so the user has some idea what's going on.
• src/hg/lib/hubConnect.c
  • lines changed 37, context: html, text, full: html, text
    add "hubClear" url variable to tell the browser to connect theassociated hub, and to disconnect from all the hubs with the same
    prefix. #13382
    
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    fixing bug where hgLiftOver would not map regions on the gbib. Also adding a progress message so the user has some idea what's going on.
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    remove tabs from short and long labels on tracks in track hubs. #13741
• src/hg/liftOver/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 38, context: html, text, full: html, text
    Loaded up DGV's update from mid-October; this is the first DGV release for hg38.Variant subtype keywords changed since last time.
    refs #14188
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 184, context: html, text, full: html, text
    Add PeptideAtlas 2014 track. refs #14054
  • lines changed 341, context: html, text, full: html, text
    Built snp142 tracks on hg19 & hg38.
    Checked for missing rs_fasta and there wasn't any this time! dbSNP provided
    a file of 1000 Genomes Phase3 indels that changed position and/or allele;
    the file had some issues and didn't come with rs_fasta changes so I decided
    to leave it as-is.
    
    hg19 still had incorrect weights for variants that uniquely mapped to a
    chrom and its alt(s); tweaked those to 1 when we didn't see MultipleAlignments.
    hg38 was OK though.
    
    refs #14189
    
  • lines changed 40, context: html, text, full: html, text
    Loaded up DGV's update from mid-October; this is the first DGV release for hg38.Variant subtype keywords changed since last time.
    refs #14188
    
  • lines changed 25, context: html, text, full: html, text
    clinvar makedoc
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 589, context: html, text, full: html, text
    Moved dbSNP tracks out of hg38/hg38.txt and into hg38/variation.txt.
  • lines changed 3, context: html, text, full: html, text
    clinvar makedoc
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 604, context: html, text, full: html, text
    Moved dbSNP tracks out of hg38/hg38.txt and into hg38/variation.txt.
  • lines changed 290, context: html, text, full: html, text
    Built snp142 tracks on hg19 & hg38.
    Checked for missing rs_fasta and there wasn't any this time! dbSNP provided
    a file of 1000 Genomes Phase3 indels that changed position and/or allele;
    the file had some issues and didn't come with rs_fasta changes so I decided
    to leave it as-is.
    
    hg19 still had incorrect weights for variants that uniquely mapped to a
    chrom and its alt(s); tweaked those to 1 when we didn't see MultipleAlignments.
    hg38 was OK though.
    
    refs #14189
    
  • lines changed 54, context: html, text, full: html, text
    Loaded up DGV's update from mid-October; this is the first DGV release for hg38.Variant subtype keywords changed since last time.
    refs #14188
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Spelling correction for modified
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    Spelling correction. Adding links to conservation track downloads to top of description page.
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.faAlign.ra
  • lines changed 107, context: html, text, full: html, text
    testing faAlign for alignments refs #14278
  • lines changed 2, context: html, text, full: html, text
    use generic Virus group to keep tagTypes happy refs #14278
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 107, context: html, text, full: html, text
    testing new sequence display refs #14278
  • lines changed 3, context: html, text, full: html, text
    testing faAlign for alignments refs #14278
  • lines changed 2, context: html, text, full: html, text
    use generic Virus group to keep tagTypes happy refs #14278
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    testing new sequence display refs #14278
  • lines changed 1, context: html, text, full: html, text
    testing faAlign for alignments refs #14278
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 1, context: html, text, full: html, text
    typo in clinvar html
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Spelling correction for modified
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
  • lines changed 4, context: html, text, full: html, text
    added italics on some et als and change a use of data is to data are
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgDnaseMasterSites.ra
  • lines changed 21, context: html, text, full: html, text
    Adding metadata and staging beta tag for wgEncodeAwgDnaseMasterSites.ra, refs #13230
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegDnaseClustered.ra
  • lines changed 27, context: html, text, full: html, text
    Adding metaData for staging release of wgEncodeRegDnaseClustered refs #13490
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegDnaseClustered.ra
  • lines changed 27, context: html, text, full: html, text
    Adding metaData for staging release of wgEncodeRegDnaseClustered refs #13490
• src/hg/makeDb/trackDb/human/hg19/trackDb.cloneEnd.ra
  • lines changed 550, context: html, text, full: html, text
    new clone ends track group
  • lines changed 16, context: html, text, full: html, text
    small changes to clone end trackDb files
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 39, context: html, text, full: html, text
    Add PeptideAtlas 2014 track. refs #14054
  • lines changed 25, context: html, text, full: html, text
    Minor tweak
  • lines changed 1, context: html, text, full: html, text
    new clone ends track group
  • lines changed 12, context: html, text, full: html, text
    Adding trackDb entries for snp142.refs #14189
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.html
  • lines changed 1, context: html, text, full: html, text
    Small typo AA-->A in html of wgEncodeAwgDnaseMasterSites refs #13230
  • lines changed 21, context: html, text, full: html, text
    Small html changes to wgEncodeAwgDnaseMasterSites.html refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.ra
  • lines changed 1, context: html, text, full: html, text
    Adding metadata and staging beta tag for wgEncodeAwgDnaseMasterSites.ra, refs #13230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    Fix incomplete URL
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Spelling correction for modified
• src/hg/makeDb/trackDb/human/hg38/trackDb.cloneEnd.ra
  • lines changed 550, context: html, text, full: html, text
    small changes to clone end trackDb files
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Adding trackDb entries for snp142.refs #14189
    
  • lines changed 2, context: html, text, full: html, text
    adding ucsc clone ends track to hg38
• src/hg/makeDb/trackDb/human/snp142.html
  • lines changed 36, context: html, text, full: html, text
    Added descriptions for snp142 tracks. refs #14189
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 467, context: html, text, full: html, text
    Added descriptions for snp142 tracks. refs #14189
• src/hg/makeDb/trackDb/human/snp142Common.html
  • lines changed 28, context: html, text, full: html, text
    Added descriptions for snp142 tracks. refs #14189
• src/hg/makeDb/trackDb/human/snp142Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Added descriptions for snp142 tracks. refs #14189
• src/hg/makeDb/trackDb/human/snp142Mult.html
  • lines changed 25, context: html, text, full: html, text
    Added descriptions for snp142 tracks. refs #14189
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    red/blue colors to clinvar, refs #14045
  • lines changed 32, context: html, text, full: html, text
    fixing broken clinvar track on the RR by adding release tags
  • lines changed 107, context: html, text, full: html, text
    Adding trackDb entries for snp142.refs #14189
    
  • lines changed 17, context: html, text, full: html, text
    Added release alpha / release beta,public stanzas for dgvPlus because dataVersion changed.refs #14188
    
• src/hg/makeDb/trackDb/joinedRmsk.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #14293
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Spelling correction for modified
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 1, context: html, text, full: html, text
    Spelling correction for modified
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #14293
• src/hg/mouseStuff/axtChain/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mouseStuff/axtToMaf/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mouseStuff/axtToPsl/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mouseStuff/lavToAxt/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mouseStuff/lavToPsl/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mouseStuff/netToAxt/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/mrnaToGene/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslCDnaFilter/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslDiff/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslHisto/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslPartition/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslSelect/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslStats/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslSwap/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/pslToBed/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/spideyToPsl/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 28, context: html, text, full: html, text
    Built snp142 tracks on hg19 & hg38.
    Checked for missing rs_fasta and there wasn't any this time! dbSNP provided
    a file of 1000 Genomes Phase3 indels that changed position and/or allele;
    the file had some issues and didn't come with rs_fasta changes so I decided
    to leave it as-is.
    
    hg19 still had incorrect weights for variants that uniquely mapped to a
    chrom and its alt(s); tweaked those to 1 when we didn't see MultipleAlignments.
    hg38 was OK though.
    
    refs #14189
    
• src/hg/utils/automation/translateDgvPlus.pl
  • lines changed 12, context: html, text, full: html, text
    Loaded up DGV's update from mid-October; this is the first DGV release for hg38.Variant subtype keywords changed since last time.
    refs #14188
    
• src/hg/utils/gff3ToGenePred/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/gff3ToPsl/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/gtfToGenePred/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 6, context: html, text, full: html, text
    red/blue colors to clinvar, refs #14045
  • lines changed 14, context: html, text, full: html, text
    changes after code review, refs #14298
• src/hg/utils/otto/clinvar/doUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    changes after code review, refs #14298
  • lines changed 1, context: html, text, full: html, text
    small bugfix for clinvar otto, refs #14045
  • lines changed 1, context: html, text, full: html, text
    bugfix for clinvar otto
• src/hg/utils/overlapSelect/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/pslMap/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/utils/refSeqGet/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/xmlToSql/test/chado/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/xmlToSql/test/hotnews/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/hg/xmlToSql/test/snp/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/product/README.customTracks.dataBase
  • lines changed 2, context: html, text, full: html, text
    add INDEX perms to customTrash db setup for narrowPeak and broadPeak custom track types refs #13823
• src/utils/bedToBigBed/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/faFilter/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/faRandomize/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/faToTwoBit/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/pslLiftSubrangeBlat/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/pslScore/tests/.gitignore
  • lines changed 2, context: html, text, full: html, text
    Adding .gitignore's for test output cruddies.
• src/utils/qa/weeklybld/boxClone
  • lines changed 80, context: html, text, full: html, text
    script for builmeister that clones the buildmeister's gbib VM into thebeta VM for QA
    
  • lines changed 42, context: html, text, full: html, text
    few changes to move the buildmeister's gbib VM into the qateam's homedir
• src/utils/qa/weeklybld/boxRelease.csh
  • lines changed 1, context: html, text, full: html, text
    removing the reference to qateam's home directory from the gbib releasescript
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v309 preview1 refs #14342

• lines changed: 4785
• files changed: 118