All File Changes

v251_base to v252_preview (2011-05-10 to 2011-05-17) v252

• python/ucscgenomics/rafile/cv/CvRaFile.py
  • lines changed 93, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/CvRaFile.pyc
  • lines changed 0, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/cvPseudo
  • lines changed 18, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/cvValidate.py
  • lines changed 81, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/cvValidate.pyc
  • lines changed 0, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/test.py
  • lines changed 5, context: html, text, full: html, text
    removed extra files in cv
• python/ucscgenomics/rafile/cv/validatescript.py
  • lines changed 4, context: html, text, full: html, text
    removed extra files in cv
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • lines changed 22, context: html, text, full: html, text
    Adding bedElements and droping the Short from RnaSeq
• src/hg/encode/DAFs/2.0/licrMm9RnaSeq.daf
  • lines changed 59, context: html, text, full: html, text
    First Version of the RNA-seq DAF for Ren Lab.
  • lines changed 5, context: html, text, full: html, text
    Added localization as a variable. Also updated validation settings to validate first 28 basepairs.
  • lines changed 2, context: html, text, full: html, text
    Fixed lab that was typed wrong when compared to cv.ra
• src/hg/encode/antibodyWikiParser.py
  • lines changed 272, context: html, text, full: html, text
    Added a new script to parse new antibody registrations out of the wiki, and download any new, approved validation documents
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 86, context: html, text, full: html, text
    Replaced the index.html page with a redirect to hgFileUi if the composite's trackDb has a fileSortOrder setting.
  • lines changed 1, context: html, text, full: html, text
    How was this missed?
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 3, context: html, text, full: html, text
    Using pigz to parallelize the compression when making a tgz.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 22, context: html, text, full: html, text
    Fixed file naming bug and added attic to mdb.txt output.
• src/hg/gsid/gsidPbGateway/gsidPbGateway.c
  • lines changed 1, context: html, text, full: html, text
    As recommended by Greg, purging bordercolor which is an obsolete MS only HTML setting. Replaced with style.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 24, context: html, text, full: html, text
    Cleaned up some not needed code.
  • lines changed 1, context: html, text, full: html, text
    Greg recommended this simplification in code review.
• src/hg/hgGateway/hgGateway.c
  • lines changed 4, context: html, text, full: html, text
    Simplifications suggested by Greg.
• src/hg/hgGene/pathways.c
  • lines changed 2, context: html, text, full: html, text
    Fixed the BioCyc URL to be variable depending on which genome the pathway belongs.
• src/hg/hgGeneRing/hgGeneRing.c
  • lines changed 3, context: html, text, full: html, text
    As recommended by Greg, purging bordercolor which is an obsolete MS only HTML setting. Replaced with style.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 11, context: html, text, full: html, text
    oops, had broken a form. All of this is going to change soon, but for demo at CSHL I need to fix it here
  • lines changed 355, context: html, text, full: html, text
    make private (now unlisted) hubs use the same status table as the public hubs, no trash use
• src/hg/hgText/hgText.c
  • lines changed 2, context: html, text, full: html, text
    As recommended by Greg, purging bordercolor which is an obsolete MS only HTML setting. Replaced with style.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    Greg recommended this simplification in code review.
• src/hg/hgTracks/hgTracks.c
  • lines changed 16, context: html, text, full: html, text
    make private (now unlisted) hubs use the same status table as the public hubs, no trash use
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    Feature #3476 (zap-to-edge arrows for OMIM tracks):Reduced spacing around next-item and next-exon/edge arrows so that next-exon/edge arrows wouldn't appear separately from exons or items that barely appear at the edge of the viewing window.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 8, context: html, text, full: html, text
    Feature #3711 bugfix: handle 0 or 1 items correctly in hacTree andVCF track handler's haplotype clustering.
  • lines changed 93, context: html, text, full: html, text
    Feature #2823 (VCF track handler): request from alpha-test user CarlosBorroto: call Belinda's coding variant functional prediction function as on the pgSnp details page.
  • lines changed 75, context: html, text, full: html, text
    Feature #3711 (VCF center-weighted haplotype clustering): David request:make the variant used as the center really stand out visually.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Simplifications suggested by Greg.
• src/hg/hgc/vcfClick.c
  • lines changed 15, context: html, text, full: html, text
    Feature #2823 (VCF track handler): request from alpha-test user CarlosBorroto: call Belinda's coding variant functional prediction function as on the pgSnp details page.
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 38, context: html, text, full: html, text
    adding Experiment Type (dataType) to the Registered Variables page, redmine 3930, also making the tables bigger to elimnate scroll bars
• src/hg/htdocs/admin/mirror.html
  • lines changed 1, context: html, text, full: html, text
    Issue 3664: Corrected the gcc version number in mirror documents.
• src/hg/htdocs/bigImage.html
  • lines changed 1098, context: html, text, full: html, text
    removing incorrect file
  • lines changed 1106, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    added encode announcement to the archives
  • lines changed 34, context: html, text, full: html, text
    adding announcement about OpenHelix Webinar
  • lines changed 2, context: html, text, full: html, text
    moved table of SNP info off left margin
  • lines changed 1, context: html, text, full: html, text
    tiny tweak: added a comma
• src/hg/htdocs/images/dot_clear.gif
  • lines changed 0, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/hg/htdocs/images/laminB1Mm9.png
  • lines changed 0, context: html, text, full: html, text
    Finished up laminB1 track for mm9
  • lines changed 0, context: html, text, full: html, text
    Final polishing on mm9's laminB1 tracks
  • lines changed 0, context: html, text, full: html, text
    Yet another mm9 laminB1 tracks descrition polishing
• src/hg/htdocs/indexNews.html
  • lines changed 84, context: html, text, full: html, text
    adding announcement about OpenHelix Webinar
  • lines changed 2, context: html, text, full: html, text
    moved table of SNP info off left margin
  • lines changed 1, context: html, text, full: html, text
    tiny tweak: added a comma
• src/hg/htdocs/style/HGStyle.css
  • lines changed 3, context: html, text, full: html, text
    Removing cursor: hand as this is only for IE < 6 and the world is moving on.
• src/hg/inc/cv.h
  • lines changed 7, context: html, text, full: html, text
    User's should see 'None' and {empty} as the same thing. Sortable tracks and sortable files lists will now show no value when term defined in cv as 'validate cv or None' and there is either no value or 'None'.
• src/hg/inc/hubConnect.h
  • lines changed 14, context: html, text, full: html, text
    make private (now unlisted) hubs use the same status table as the public hubs, no trash use
• src/hg/inc/pgSnp.h
  • lines changed 10, context: html, text, full: html, text
    Feature #2823 (VCF track handler): request from alpha-test user CarlosBorroto: call Belinda's coding variant functional prediction function as on the pgSnp details page.
• src/hg/js/ajax.js
  • lines changed 4, context: html, text, full: html, text
    Fix for redmine 3914. The metadata '...' had messed up coloring.
• src/hg/js/utils.js
  • lines changed 14, context: html, text, full: html, text
    Fix for redmine 3914. The metadata '...' had messed up coloring.
• src/hg/lib/customFactory.c
  • lines changed 40, context: html, text, full: html, text
    consolidate the progress write to a subroutine
• src/hg/lib/cv.c
  • lines changed 36, context: html, text, full: html, text
    User's should see 'None' and {empty} as the same thing. Sortable tracks and sortable files lists will now show no value when term defined in cv as 'validate cv or None' and there is either no value or 'None'.
• src/hg/lib/fileUi.c
  • lines changed 2, context: html, text, full: html, text
    Changed rsync command that verifies file existance to not recurse, confuse with symlinks or verbosify too much.
  • lines changed 3, context: html, text, full: html, text
    User's should see 'None' and {empty} as the same thing. Sortable tracks and sortable files lists will now show no value when term defined in cv as 'validate cv or None' and there is either no value or 'None'.
• src/hg/lib/hVarSubst.c
  • lines changed 1, context: html, text, full: html, text
    As recommended by Greg, purging bordercolor which is an obsolete MS only HTML setting. Replaced with style.
• src/hg/lib/hubConnect.c
  • lines changed 92, context: html, text, full: html, text
    make private (now unlisted) hubs use the same status table as the public hubs, no trash use
• src/hg/lib/hui.c
  • lines changed 69, context: html, text, full: html, text
    Removing some old #ifndef code that has been unused for 6 months.
  • lines changed 7, context: html, text, full: html, text
    User's should see 'None' and {empty} as the same thing. Sortable tracks and sortable files lists will now show no value when term defined in cv as 'validate cv or None' and there is either no value or 'None'.
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    Fixed SNP expandable checkbox groups title from jumping right whehn a group is expanded.
  • lines changed 9, context: html, text, full: html, text
    Last fix to SNPs Expandable options worked in IE in compatability mode but not IE8. Now it does.
• src/hg/lib/mdb.c
  • lines changed 6, context: html, text, full: html, text
    Fixed a couple of bug in mdbUpte: encodeExp was updating accession without it being requested and using -var and delete was segfaulting.
• src/hg/lib/omimAv.as
  • lines changed 12, context: html, text, full: html, text
    Created omimAv.as.
• src/hg/lib/omimAvRepl.as
  • lines changed 10, context: html, text, full: html, text
    Created omimAvRepl.as.
• src/hg/lib/omimDisorderMap.as
  • lines changed 9, context: html, text, full: html, text
    Created omimDisorderMap.as.
• src/hg/lib/omimDisorderPhenotype.as
  • lines changed 11, context: html, text, full: html, text
    Created omimDisorderPhenotype.as.
• src/hg/lib/omimGeneSymbol.as
  • lines changed 6, context: html, text, full: html, text
    Created omimGeneSymbol.as.
• src/hg/lib/pgSnp.c
  • lines changed 98, context: html, text, full: html, text
    Feature #2823 (VCF track handler): request from alpha-test user CarlosBorroto: call Belinda's coding variant functional prediction function as on the pgSnp details page.
• src/hg/lib/trackHub.c
  • lines changed 4, context: html, text, full: html, text
    make private (now unlisted) hubs use the same status table as the public hubs, no trash use
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 205, context: html, text, full: html, text
    beginning 7-way alignment
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 70, context: html, text, full: html, text
    Finished gap, genbank steps
  • lines changed 15, context: html, text, full: html, text
    Finished ctgPos2 track for Cow bosTau6
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 41, context: html, text, full: html, text
    corrected annotated maf creation
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 1423, context: html, text, full: html, text
    make release notes for caltech rnaseq release 2
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 254, context: html, text, full: html, text
    redmine 3880: rework the felCat4 multiz6way due to mafAddIRows error (3494)
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    Updated omimAv table build by ignoring the head line.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 15, context: html, text, full: html, text
    finished laminB1 track for mm9
  • lines changed 58, context: html, text, full: html, text
    Use viewLimits -1.5:1.5 for mm9's laminB1 tracks
  • lines changed 6, context: html, text, full: html, text
    Final polishing on mm9's laminB1 tracks
  • lines changed 3, context: html, text, full: html, text
    Yet another mm9 laminB1 tracks descrition polishing
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 218, context: html, text, full: html, text
    rerunning the annotation of the 6way to avoid mafAddIRows
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bosTau6 - Cow
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    Added bosTau6
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added bosTau6 - Cow
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 62, context: html, text, full: html, text
    Fixed a couple of bug in mdbUpte: encodeExp was updating accession without it being requested and using -var and delete was segfaulting.
  • lines changed 145, context: html, text, full: html, text
    Added -setVal for vals with spaces. Now object selection should be identical to mdbPrint with -var/-val only for slection.
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Finished ctgPos2 track for Cow bosTau6
  • lines changed 6, context: html, text, full: html, text
    Added more lines for new OMIM tables.
  • lines changed 1, context: html, text, full: html, text
    Added one rule for omimLocationID.
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 2, context: html, text, full: html, text
    remove comment about None row in gene table
• src/hg/makeDb/trackDb/cow/bosTau6/ctgPos2.html
  • lines changed 15, context: html, text, full: html, text
    Finished ctgPos2 track for Cow bosTau6
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Finished ctgPos2 track for Cow bosTau6
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Replaced auxUnValid with auxSup to prevent confusion over 'UnValid'
  • lines changed 1, context: html, text, full: html, text
    Added term id that was missing for TReg cell line. Should mathc same termId (ontology) as TNaive.
  • lines changed 22, context: html, text, full: html, text
    Added cell line B-cell_(CD43-) and strain Spretus.BL6-Xist so that UW Mouse DNase data can be loaded.
  • lines changed 2, context: html, text, full: html, text
    Updated age of the B-cells harvested to adult-8wks since they were harvested from adult mice and are not a cell line.
  • lines changed 2, context: html, text, full: html, text
    Changing the case of human and mouse, so that the validation will work
  • lines changed 1, context: html, text, full: html, text
    changed the mouse stanza to type organism, as it should've been
  • lines changed 107, context: html, text, full: html, text
    Added three new antibodies. Changed the case of the organism Human and Mouse in various places, to facilitate validation
  • lines changed 2, context: html, text, full: html, text
    Fixed statza for H3K9me3_(9754) to have a term filed instead of erm field.
  • lines changed 410, context: html, text, full: html, text
    Post code review check-in. This includes a huge number of changes, based on incorporating the NHGRI-curated spreadsheet modifications, as entered by Cricket and reviewed by Jeff
  • lines changed 2, context: html, text, full: html, text
    Update tags for auxValid and auxExp to be lower case to follow convention of either tags all in Upper or Lower case. Extended tags to be auxval and auxexp to match tag for auxSup of auxsup.
  • lines changed 115, context: html, text, full: html, text
    Back-filled the age and strain in mouse tissues to Unknown, as appropriate, so that the lack of age or strain won't be tagged by the validator
  • lines changed 403, context: html, text, full: html, text
    NHGRI edits plus some updates
  • lines changed 1, context: html, text, full: html, text
    Removed extra line space left in cv.ra
  • lines changed 29, context: html, text, full: html, text
    Added PMID links to satisfy Redmine # 2711
  • lines changed 69, context: html, text, full: html, text
    Back-filled the order URLs for several mouse tissue entries, for validation purposes. These are mouse cell types that are produced within the lab, and the order URL is essentially the lab itself
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 807, context: html, text, full: html, text
    releasing cv.ra changes to RR
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/autoExpDcc.pl
  • lines changed 100, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
  • lines changed 100, context: html, text, full: html, text
    recursive add directory accidentely captured my script to add, removed them
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/list.txt
  • lines changed 29, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
  • lines changed 29, context: html, text, full: html, text
    recursive add directory accidentely captured my script to add, removed them
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/list2.txt
  • lines changed 1, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
  • lines changed 1, context: html, text, full: html, text
    recursive add directory accidentely captured my script to add, removed them
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Removing reference to YaleRNASeq as we are dropping this composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 105, context: html, text, full: html, text
    Added expId's
  • lines changed 1, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 3, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 283, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 26, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 56, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
  • lines changed 59, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 35, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 117, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 7, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 7, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 86, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 12, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 2, context: html, text, full: html, text
    added expId
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra
  • lines changed 5, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 80, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 8, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 68, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 556, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • lines changed 29, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 371, context: html, text, full: html, text
    Added ExpId's according the what the redmine ticket #3921
• src/hg/makeDb/trackDb/human/hg19/acembly.html
  • lines changed 4, context: html, text, full: html, text
    Made minor changes per code review, issue 3900, having to do with punctuation, and the label for one link.
• src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
  • lines changed 1, context: html, text, full: html, text
    dropped an errant < symbol
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 773, context: html, text, full: html, text
    Adding new data, changing long labeles, Sorting by Tier
  • lines changed 302, context: html, text, full: html, text
    Adding more submissions
  • lines changed 1093, context: html, text, full: html, text
    Cleaning up the metaDb to match the downloads files and to have consistent terms
  • lines changed 527, context: html, text, full: html, text
    Changed short labels, changed dates to reflect original hg18 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 547, context: html, text, full: html, text
    Adding all of the ExonGencV3c
  • lines changed 458, context: html, text, full: html, text
    Added new submissions for HepG2, A549 and MCF7
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 10, context: html, text, full: html, text
    Updated GEO accession numbers to reflect corrections made
  • lines changed 809, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 3, context: html, text, full: html, text
    Added expId and dccAccession to Anshul's mapability track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 7, context: html, text, full: html, text
    Added attic term to the validation files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 3, context: html, text, full: html, text
    Added attic term to the validation files
  • lines changed 201, context: html, text, full: html, text
    added in files from submission Id#4107, then fixed the filenames for the download.
  • lines changed 23, context: html, text, full: html, text
    Added ExpId's and dccAccessions to OpenChromDnase's metaDb entry
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 3, context: html, text, full: html, text
    Added attic term to the validation files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 217, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 82, context: html, text, full: html, text
    added ExpId's to SydhHistone
  • lines changed 82, context: html, text, full: html, text
    dccAccession numbers magically appeared, adding them in now.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 137, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 5, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 243, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1515, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1515, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 967, context: html, text, full: html, text
    Added expId's and dccAccession number to track according to #3693
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    added accession numbers to yaleRnaSeq
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 9, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra
  • lines changed 1, context: html, text, full: html, text
    Added dragAndDrop subtracks so that the color bug does not show
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 64, context: html, text, full: html, text
    Merged Georgis changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 278, context: html, text, full: html, text
    Adding new data, changing long labeles, Sorting by Tier
  • lines changed 18, context: html, text, full: html, text
    Adding more submissions
  • lines changed 167, context: html, text, full: html, text
    Changed short labels, changed dates to reflect original hg18 submissions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 137, context: html, text, full: html, text
    Added new submissions for HepG2, A549 and MCF7
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 1, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 2, context: html, text, full: html, text
    Forgot noInherit on
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 1, context: html, text, full: html, text
    added dccAccessions to tracks that were in the pushQ but didn't have it, and modified trackDb accordingly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 19, context: html, text, full: html, text
    Made the Description clearer about what certain histone modificiation represent phenotypically. Redmine #68 issue # 24.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Added dccaccession to the filesortorder for SydhHistone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 15, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 1, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 4027, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 2195, context: html, text, full: html, text
    Added dccAccession to the file sort order for the tracks listed in #3693, updated trackDb.wgEncode.ra to match, created .new files where required
• src/hg/makeDb/trackDb/human/laminB1Super.html
  • lines changed 1, context: html, text, full: html, text
    Fixed redmine 3934 bug: Disappered NKI Nuc Lamina tracks after refresh button is clicked
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changed region from 100000 to 100000, because of 'window out of range' error
• src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
  • lines changed 125, context: html, text, full: html, text
    Finished up laminB1 track for mm9
  • lines changed 1, context: html, text, full: html, text
    Final polishing on mm9's laminB1 tracks
  • lines changed 8, context: html, text, full: html, text
    Yet another mm9 laminB1 tracks descrition polishing
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added 10 experiments for the Ren lab RNA-Seq track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 18, context: html, text, full: html, text
    Added tissueSourceType information for MEF cells, that were forgotten.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 1541, context: html, text, full: html, text
    Added 10 experiments for the Ren lab RNA-Seq track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 24, context: html, text, full: html, text
    Added tissueSourceType information for MEF cells, that were forgotten.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1405, context: html, text, full: html, text
    Added 14 submissions to track.
  • lines changed 69, context: html, text, full: html, text
    Updated the naming of files Rep 1 of 3134 experiment to have correct strain: RIII and age:Immortal in the file name.
  • lines changed 58, context: html, text, full: html, text
    Changed Raw Signal -> Signal to better describe data as presented. Redmine #191.
  • lines changed 171, context: html, text, full: html, text
    renamed Raw to Sig for .bigwig files
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Finished up laminB1 track for mm9
  • lines changed 8, context: html, text, full: html, text
    Use viewLimits -1.5:1.5 for mm9's laminB1 tracks
  • lines changed 4, context: html, text, full: html, text
    Final polishing on mm9's laminB1 tracks
  • lines changed 1, context: html, text, full: html, text
    Yet another mm9 laminB1 tracks descrition polishing
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    Added 10 experiments for the Ren lab RNA-Seq track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 14, context: html, text, full: html, text
    Updated track description pages of tracks to reflect edits desired by the lab.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
  • lines changed 107, context: html, text, full: html, text
    Added track Description for the LICR RNA-Seq track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 413, context: html, text, full: html, text
    Added 10 experiments for the Ren lab RNA-Seq track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 14, context: html, text, full: html, text
    Updated track description pages of tracks to reflect edits desired by the lab.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 2, context: html, text, full: html, text
    Changed Raw Signal -> Signal to better describe data as presented. Redmine #191.
  • lines changed 8, context: html, text, full: html, text
    Added Another Refernece journal, Redmine #191.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 356, context: html, text, full: html, text
    Added 14 submissions to track.
  • lines changed 3, context: html, text, full: html, text
    Updated the naming of files Rep 1 of 3134 experiment to have correct strain: RIII and age:Immortal in the file name.
  • lines changed 119, context: html, text, full: html, text
    Changed Raw Signal -> Signal to better describe data as presented. Redmine #191.
  • lines changed 165, context: html, text, full: html, text
    Updated coloring schema. This is the first pass.
  • lines changed 100, context: html, text, full: html, text
    renamed Raw to Sig for .bigwig files
  • lines changed 1, context: html, text, full: html, text
    Recommented out line that was undone to use renamer.
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 9, context: html, text, full: html, text
    update gene translation table
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 1, context: html, text, full: html, text
    changed don't to do not
• src/hg/oneShot/parseOmimDisorder/makefile
  • lines changed 14, context: html, text, full: html, text
    Created makefile.
• src/hg/oneShot/parseOmimDisorder/parseOmimDisorder.c
  • lines changed 228, context: html, text, full: html, text
    Created parseOmimDisorder.c.
• src/hg/protein/pbGateway/pbGateway.c
  • lines changed 1, context: html, text, full: html, text
    As recommended by Greg, purging bordercolor which is an obsolete MS only HTML setting. Replaced with style.
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 2, context: html, text, full: html, text
    Simplifications suggested by Greg.
• src/hg/txGraph/txBedToGraph/makeGraph.c
  • lines changed 72, context: html, text, full: html, text
    Fixed a bug involving removing double-soft edges that are embedded in a double-hard or half-hard edge. The range tree that was collecting the ranges of hard edges contained a pointer to only the edge added most recently. When a double soft was found that fell within the range, it was merged with the edge for the range. The problem was that the coordinates of the edge might be a subset of the coordinates of the range. So, when the evidence for the double-soft edge was assigned to the range, it was potentially assigned to an edge that it didn't overlap. To address this, in the range nodes, I'm collecting a singly-linked list of all candidate hard edges. When a double soft is found to fall within a range, I look for a single edge that it falls within. If I find such an edge, then I reassign the evidence
  • lines changed 2, context: html, text, full: html, text
    Changing lowercase "true" and "false" to uppercase, because that isdefined in common.h. Using lowercase does not cause a compilation error on our CentOs dev systems, but it does on Ubuntu.
• src/hg/visiGene/hgVisiGene/README
  • lines changed 2, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/hg/visiGene/hgVisiGene/bigImage.html
  • lines changed 20, context: html, text, full: html, text
    getting visiGene to work with html 4.01 transitional
  • lines changed 1106, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/hg/visiGene/hgVisiGene/dot_clear.gif
  • lines changed 0, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 9, context: html, text, full: html, text
    Fixing height of image box in IE >= 8.
  • lines changed 2, context: html, text, full: html, text
    Sorry, this last bit may be just what the doctor ordered to ensure the image gets resized properly.
  • lines changed 8, context: html, text, full: html, text
    The image size/centering problem was solved on IE>=8 but there were sizing issues on Mac FF, so I am generalizing the code to all browsers other than IE<8. There is still an issue with the purple box in the left frame showing the portion of the image currently seen in the right frame. This is in FF and Chrome but not IE. All this is for redmine 3933
  • lines changed 31, context: html, text, full: html, text
    getting visiGene to work with html 4.01 transitional
• src/hg/visiGene/hgVisiGene/makefile
  • lines changed 9, context: html, text, full: html, text
    now that htdocs is in kent source I have moved bigImage.html and dot_clear.gif to the expected locations.
• src/lib/hacTree.c
  • lines changed 11, context: html, text, full: html, text
    Feature #3711 bugfix: handle 0 or 1 items correctly in hacTree andVCF track handler's haplotype clustering.
• src/lib/net.c
  • lines changed 18, context: html, text, full: html, text
    require FTP to check for return code of 331 before sending the PASS command.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 13, context: html, text, full: html, text
    add the ability to have tab separated fields
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v252 preview1

• lines changed: 33708
• files changed: 240