All File Changes

v247_base to v248_preview (2011-02-14 to 2011-02-22) v248

• python/ucscgenomics/rafile/filter.ra
  • lines changed 9, context: html, text, full: html, text
    updated rafile and first pass on raInspect
• python/ucscgenomics/rafile/filterFile.py
  • lines changed 101, context: html, text, full: html, text
    updated rafile and first pass on raInspect
• python/ucscgenomics/rafile/raInspect.py
  • lines changed 72, context: html, text, full: html, text
    updated rafile and first pass on raInspect
• python/ucscgenomics/rafile/radict.py
  • lines changed 73, context: html, text, full: html, text
    updated rafile and first pass on raInspect
• src/hg/encode/DAFs/2.0/caltechElements.daf
  • lines changed 70, context: html, text, full: html, text
    Added a new set of Elements files
• src/hg/encode/DAFs/2.0/rikenElements.daf
  • lines changed 7, context: html, text, full: html, text
    Added clusters view
• src/hg/encode/autoSql/bedRnaElements.as
  • lines changed 13, context: html, text, full: html, text
    hmm... thought I'd moved this into place
• src/hg/encode/autoSql/rnaElements.as
  • lines changed 13, context: html, text, full: html, text
    Creating new format
  • lines changed 13, context: html, text, full: html, text
    this is called bedRnaElements.as now
• src/hg/encode/docId/docIdSubmitDir/docIdSubmitDir.c
  • lines changed 4, context: html, text, full: html, text
    add cell name to names. This needs to be fixed to use the tag instead of the term to remove the special characters
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 4, context: html, text, full: html, text
    add cell name to names. This needs to be fixed to use the tag instead of the term to remove the special characters
• src/hg/encode/docId/inc/docId.h
  • lines changed 1, context: html, text, full: html, text
    add cell name to names. This needs to be fixed to use the tag instead of the term to remove the special characters
• src/hg/encode/docId/lib/docIdSub.c
  • lines changed 2, context: html, text, full: html, text
    add cell name to names. This needs to be fixed to use the tag instead of the term to remove the special characters
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 5, context: html, text, full: html, text
    let bedRnaElements have a NULL field
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 3, context: html, text, full: html, text
    Updated usage
• src/hg/encode/encodeStatus/encodeStatus.pl
  • lines changed 5, context: html, text, full: html, text
    Added status Revoked
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 13, context: html, text, full: html, text
    Adding md5sum and bioRep as fields in fields.ra and md5sum in cv.ra
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    Added bioRep and md5sum as valid fields
  • lines changed 1, context: html, text, full: html, text
    add bedRnaElements
  • lines changed 1, context: html, text, full: html, text
    make check for GTF not look into the hierarchy. This is stop-gap until we get GTF validation into validateFiles
• src/hg/hgTables/bam.c
  • lines changed 15, context: html, text, full: html, text
    Fixing bug found while playing w/hgTables for Code Review #2840(not caused by Brian's changes): BAM tracks can have separate BAM files per chromosome, in which case the db table has an extra column seqName, so bigWigFileName() won't return the correct fileName for those tracks. Share bigWigFileName's logic for detecting custom track or hub track, and use bamFile.h's bamFileNameFromTable() for database tables.
• src/hg/hgTables/bigWig.c
  • lines changed 12, context: html, text, full: html, text
    Fixing bug found while playing w/hgTables for Code Review #2840(not caused by Brian's changes): BAM tracks can have separate BAM files per chromosome, in which case the db table has an extra column seqName, so bigWigFileName() won't return the correct fileName for those tracks. Share bigWigFileName's logic for detecting custom track or hub track, and use bamFile.h's bamFileNameFromTable() for database tables.
• src/hg/hgTables/hgTables.h
  • lines changed 8, context: html, text, full: html, text
    Fixing bug found while playing w/hgTables for Code Review #2840(not caused by Brian's changes): BAM tracks can have separate BAM files per chromosome, in which case the db table has an extra column seqName, so bigWigFileName() won't return the correct fileName for those tracks. Share bigWigFileName's logic for detecting custom track or hub track, and use bamFile.h's bamFileNameFromTable() for database tables.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    handle bamWigs
• src/hg/hgTracks/bamTrack.c
  • lines changed 116, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
  • lines changed 2, context: html, text, full: html, text
    Moving udc cache timeout code from bamTrack.c to hgTracks.c so it's with the other udc cache call. Making a udcTimeout cart variable that controls the length of it rather than having a hardcoded 300 seconds. (Still defaults to 300).
• src/hg/hgTracks/bedTrack.c
  • lines changed 2, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    Moving udc cache timeout code from bamTrack.c to hgTracks.c so it's with the other udc cache call. Making a udcTimeout cart variable that controls the length of it rather than having a hardcoded 300 seconds. (Still defaults to 300).
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
• src/hg/hgTracks/simpleTracks.c
  • lines changed 68, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    a complicated commit to support the arrows in decipher tracks, next item buttons on bigBeds, and the beginnings of BAM wiggles
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    Removed PI from Caltech description, redmine #35
• src/hg/htdocs/ENCODE/index.html
  • lines changed 50, context: html, text, full: html, text
    Add news for recent tracks
  • lines changed 2, context: html, text, full: html, text
    Update Mouse sectino
  • lines changed 1, context: html, text, full: html, text
    correcting the Read More date on index page, correcting the corresponding date tag on the archives page
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    Add news for recent tracks
  • lines changed 1, context: html, text, full: html, text
    correcting the Read More date on index page, correcting the corresponding date tag on the archives page
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 52, context: html, text, full: html, text
    Added item about links to knownCanonical transcripts in browser. (Part of Redmine #2372)
  • lines changed 3, context: html, text, full: html, text
    Added org to example URL (even tho not needed) to avoid confusion, since it refers to other example that has org present.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 26, context: html, text, full: html, text
    Added info about drag/reorder, moved drag/zoom info to a different section.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 21, context: html, text, full: html, text
    Added 3 new pubs.
  • lines changed 5, context: html, text, full: html, text
    Added pub by Melissa.
• src/hg/inc/bamFile.h
  • lines changed 2, context: html, text, full: html, text
    Tweaked comment describing bamFileNameFromTable().
• src/hg/inc/genePred.h
  • lines changed 4, context: html, text, full: html, text
    start => chromStart in parameter lists; fix bug in codonToPos (cdsEnd s/d be cdsStart)
• src/hg/js/hgTracks.js
  • lines changed 17, context: html, text, full: html, text
    make sure l and r values are in open & show details... links (fixes redmine #2896)
• src/hg/lib/bamFile.c
  • lines changed 2, context: html, text, full: html, text
    Tweaked comment describing bamFileNameFromTable().
• src/hg/lib/genbank.c
  • lines changed 1, context: html, text, full: html, text
    Updated the code that checks for selenocysteine exceptions, to match some apparent changes in the format of the selenocysteine exception entries
• src/hg/lib/genePred.c
  • lines changed 10, context: html, text, full: html, text
    start => chromStart in parameter lists; fix bug in codonToPos (cdsEnd s/d be cdsStart)
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 16, context: html, text, full: html, text
    A couple of tracks had changed, updated Notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release1.notes
  • lines changed 77, context: html, text, full: html, text
    New realese notes with dropped data
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 145, context: html, text, full: html, text
    New realese notes with dropped data
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 693, context: html, text, full: html, text
    Initial setup for Turkey melGal1
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 277, context: html, text, full: html, text
    Initial myoLuc2 (Microbat assembly)
  • lines changed 11, context: html, text, full: html, text
    Set default location for microbat myoLuc2
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 4, context: html, text, full: html, text
    reload the all_mrna table
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 242, context: html, text, full: html, text
    initial db build for chimp
  • lines changed 326, context: html, text, full: html, text
    finished with repeatMasker
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 7, context: html, text, full: html, text
    Added myoLuc2
  • lines changed 6, context: html, text, full: html, text
    Set melGal1.perChromTables = no
  • lines changed 19, context: html, text, full: html, text
    Added macEug2
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • lines changed 9, context: html, text, full: html, text
    add an option to convert a '.' into a NULL in the specified field
• src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
  • lines changed 2, context: html, text, full: html, text
    adding VmPeak printout to check memory usage
• src/hg/makeDb/hgLoadWiggle/hgWiggle.c
  • lines changed 2, context: html, text, full: html, text
    adding VmPeak printout to check memory usage
• src/hg/makeDb/hgLoadWiggle/wigEncode.c
  • lines changed 3, context: html, text, full: html, text
    adding VmPeak printout to check memory usage
• src/hg/makeDb/trackDb/README
  • lines changed 2, context: html, text, full: html, text
    Just a mention of two new trackDb settings in the README
  • lines changed 11, context: html, text, full: html, text
    clarify bigBed and bigWig loading instructions
• src/hg/makeDb/trackDb/chicken/galGal2/rnaGene.html
  • lines changed 1, context: html, text, full: html, text
    updated link to tRNAscan-SE website
• src/hg/makeDb/trackDb/chimp/panTro3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial contents from makeGenomeDb
  • lines changed 182, context: html, text, full: html, text
    edited contents for description gold and gap html pages
• src/hg/makeDb/trackDb/chimp/panTro3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial contents from makeGenomeDb
  • lines changed 61, context: html, text, full: html, text
    edited contents for description gold and gap html pages
• src/hg/makeDb/trackDb/chimp/panTro3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial contents from makeGenomeDb
  • lines changed 32, context: html, text, full: html, text
    edited contents for description gold and gap html pages
  • lines changed 1, context: html, text, full: html, text
    add chrM
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    initial contents from makeGenomeDb
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 32, context: html, text, full: html, text
    Removed two duplicated antibodies. IRF4 duplicates IRF4_(M-17), and EBF duplicates EBF1_(C-8). Thanks to some metadata updates by Venkat, these antibodies are no longer used in the metadata for any track, and (hopefully) can be removed now with no adverse consequences
  • lines changed 10, context: html, text, full: html, text
    Removed priority from md5sum
  • lines changed 3, context: html, text, full: html, text
    Changed the tag for longNonPolyA to Pam to match Pap
• src/hg/makeDb/trackDb/human/decipherOld.html
  • lines changed 67, context: html, text, full: html, text
    changing html for decipher track to be new html in preparation to release hg18 and hg19 http://redmine.soe.ucsc.edu/issues/2719
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    putting agilent CGH track in variation group for hg18, mm9 and rn4. Had to change priorities for mm9 and rn4 so that it showed up after SNPs. http://redmine.soe.ucsc.edu/issues/1791
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 24, context: html, text, full: html, text
    Added accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed the issues from redmine ticket 2254 note 6
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 59, context: html, text, full: html, text
    Removed antibody Input from control to be consistent with use of antibody control across all experiments. Also removed duplicate files and metadata for 2 fastq's: wgEncodeHaibTfbsGm12878InputPcr1xRawDataRep1 and wgEncodeHaibTfbsGm12878InputPcr1xRawDataRep2.
  • lines changed 183, context: html, text, full: html, text
    Added missing experiment GM12878 YY1 to display.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 63, context: html, text, full: html, text
    Added missing origAssembly as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 132, context: html, text, full: html, text
    Added missing origAssembly as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 87, context: html, text, full: html, text
    Added missing origAssembly as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 553, context: html, text, full: html, text
    Removing 6 experiments at request of the lab
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 127, context: html, text, full: html, text
    Fixed all of the GeneST to GeneSt, hopefully
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 475, context: html, text, full: html, text
    Fixed all of the GeneST to GeneSt, hopefully
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed typo of dateReubmitted -> dateResubmitted.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 571, context: html, text, full: html, text
    Upgraded to using the new hgFileUi cgi. As a result filled in missing treatment values in metaDb. Also, added new html page to remove refrences to downloads page, as track description in now present on hgFileUi page.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaSeq.ra
  • lines changed 156, context: html, text, full: html, text
    staging revised metadata on beta: Geo accessions, entries for additional files, dataVersion corrections
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 6112, context: html, text, full: html, text
    going to replace this file with the updated version
  • lines changed 6105, context: html, text, full: html, text
    replaced old file with the updated version for RIKEN, redmine issue #41
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaSeq.ra
  • lines changed 156, context: html, text, full: html, text
    releasing revised metadata to RR: Geo accessions, entries for additional files, dataVersion corrections
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    changing the Agilent CGH track to be in the Variation Group and to have the name 'Arrays' instead per http://redmine.soe.ucsc.edu/issues/1791
  • lines changed 10, context: html, text, full: html, text
    add a bamWig track
  • lines changed 8, context: html, text, full: html, text
    adding hg18-ball logo as well as details on track description page for sestan brain and genome variants track (previously lifted tracks). Adding details on track description for affy RNA Loc track since couldn't get hg19-ball logo to appear. http://redmine.soe.ucsc.edu/issues/1730
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 1, context: html, text, full: html, text
    adding hg18-ball logo as well as details on track description page for sestan brain and genome variants track (previously lifted tracks). Adding details on track description for affy RNA Loc track since couldn't get hg19-ball logo to appear. http://redmine.soe.ucsc.edu/issues/1730
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 6, context: html, text, full: html, text
    Changed the Long and Short Labels for Tiling at Kate's request
  • lines changed 214, context: html, text, full: html, text
    Added 4 more submissions, removed the paried label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Changed Wold to Caltech
  • lines changed 1, context: html, text, full: html, text
    Changed Wold to Caltech
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 21, context: html, text, full: html, text
    New track description from lab.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 33, context: html, text, full: html, text
    Merged new submissions with encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.html
  • lines changed 122, context: html, text, full: html, text
    MethylArray data is Methyl27
  • lines changed 80, context: html, text, full: html, text
    New track description from lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 5, context: html, text, full: html, text
    changed sort order of cells
  • lines changed 60, context: html, text, full: html, text
    Matched files for encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylArray.html
  • lines changed 122, context: html, text, full: html, text
    MethylArray data is Methyl27
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylArray.ra
  • lines changed 759, context: html, text, full: html, text
    Methyl27 is being used instead of MethylArray
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 100, context: html, text, full: html, text
    New track description from lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 9, context: html, text, full: html, text
    Fixed the issues from redmine ticket 2254 note 6
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    set max windows to 1M
  • lines changed 1, context: html, text, full: html, text
    maxWindowsToDraw to maxWindowToDraw
  • lines changed 8, context: html, text, full: html, text
    Fixed the issues from redmine ticket 2254 note 6
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 40, context: html, text, full: html, text
    Added missing experiment GM12878 YY1 to display.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 7, context: html, text, full: html, text
    fixed typos, misspellings, and minor formatting
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 60, context: html, text, full: html, text
    Changed sort order as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 22, context: html, text, full: html, text
    Changed sort order as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 31, context: html, text, full: html, text
    Changed sort order as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 7, context: html, text, full: html, text
    Changed sort order as per Katrina's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRIPSuper.html
  • lines changed 88, context: html, text, full: html, text
    Beginning draft for Melissa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
  • lines changed 90, context: html, text, full: html, text
    Added a supertrack description page for RNA-Binding Protein experiments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 13, context: html, text, full: html, text
    Fixed link to point to hg18, moved release notes after methods and reworded it, redmine issue#41
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 4, context: html, text, full: html, text
    Changing the maxWindowToDraw setting and the sutoscale and the title
  • lines changed 1, context: html, text, full: html, text
    Changing the maxWindowToDraw setting to very low for the alignments
  • lines changed 180, context: html, text, full: html, text
    Removing 6 experiments at request of the lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 4, context: html, text, full: html, text
    Changing the maxWindowToDraw setting and the sutoscale and the title
  • lines changed 1, context: html, text, full: html, text
    Changing the maxWindowToDraw setting to very low for the alignments
  • lines changed 180, context: html, text, full: html, text
    Removing 6 experiments at request of the lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneST.html
  • lines changed 157, context: html, text, full: html, text
    Changed file name so that it matched trackDb.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 157, context: html, text, full: html, text
    Changed file name so that it matched trackDb.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the Long and Short Labels for Tiling at Kate's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the display of the wgEncodeSydhTfbsGm12878Xrcc4IggmusSig to be WHIP as it should be and not Xrcc4.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
  • lines changed 147, context: html, text, full: html, text
    Removed the following sentence 'Data have been normalized to 25 million reads per cell type.' on instructions from lab. The data has not been normalized.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 1, context: html, text, full: html, text
    Upgraded Downloads page to use new hgFileUi and fileSortOrder.
  • lines changed 3, context: html, text, full: html, text
    Removed dataVersion, as this is out of date. Added new html reference. Moved cell lines display from horizontal to vertical.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 113, context: html, text, full: html, text
    Upgraded to using the new hgFileUi cgi. As a result filled in missing treatment values in metaDb. Also, added new html page to remove refrences to downloads page, as track description in now present on hgFileUi page.
  • lines changed 1, context: html, text, full: html, text
    Removed the following sentence 'Data have been normalized to 25 million reads per cell type.' on instructions from lab. The data has not been normalized.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
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    Upgraded to using the new hgFileUi cgi. As a result filled in missing treatment values in metaDb. Also, added new html page to remove refrences to downloads page, as track description in now present on hgFileUi page.
  • lines changed 3, context: html, text, full: html, text
    Removed dataVersion, as this is out of date. Added treatment to sortOrder and renamed subgroup for HUVEC so that it is pairing with other HUVEC cells.
  • lines changed 4, context: html, text, full: html, text
    Updated display of Hotspots and peaks from pack to dense.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 7, context: html, text, full: html, text
    Removed the implied dataVersion in trackDb. Also set Hotspots and Peaks to dense as requested by the lab.
  • lines changed 29, context: html, text, full: html, text
    Added back missing AoAf Replicate 1 data.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changing html for decipher track to be new html in preparation to release hg18 and hg19 http://redmine.soe.ucsc.edu/issues/2719
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding panTro3 to the build
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    putting agilent CGH track in variation group for hg18, mm9 and rn4. Had to change priorities for mm9 and rn4 so that it showed up after SNPs. http://redmine.soe.ucsc.edu/issues/1791
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    putting agilent CGH track in variation group for hg18, mm9 and rn4. Had to change priorities for mm9 and rn4 so that it showed up after SNPs. http://redmine.soe.ucsc.edu/issues/1791
• src/hg/mouseStuff/axtChain/axtChain.c
  • lines changed 10, context: html, text, full: html, text
    added sanity check for blocks being in range of sequence
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 10, context: html, text, full: html, text
    make non split gold gap the default
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 5, context: html, text, full: html, text
    add an option to do simple checking on input as stop-gap for GTF acceptance in ENCODE pipeline
• src/inc/net.h
  • lines changed 10, context: html, text, full: html, text
    added alternate method for finding filesize via byterange, useful workaround for udc used against poorly configured remote apache servers
• src/lib/memalloc.c
  • lines changed 2, context: html, text, full: html, text
    allow up to 16 Gb of allocation for needLargeMem() on 64 bit machines
• src/lib/net.c
  • lines changed 40, context: html, text, full: html, text
    added alternate method for finding filesize via byterange, useful workaround for udc used against poorly configured remote apache servers
  • lines changed 1, context: html, text, full: html, text
    oops, now need to pass the full url with byterange so that it will expect 206 partial content response
• src/lib/udc.c
  • lines changed 8, context: html, text, full: html, text
    added alternate method for finding filesize via byterange, useful workaround for udc used against poorly configured remote apache servers
• src/utils/bigWigSummary/bigWigSummary.c
  • lines changed 1, context: html, text, full: html, text
    add a note about start and end coordinates being in BED format
• src/utils/git-reports/git-reports.c
  • lines changed 2, context: html, text, full: html, text
    take out the generic Merge commits
• src/utils/qa/countPerChrom.csh
  • lines changed 9, context: html, text, full: html, text
    added comments. added extra debug around rm files. changed a hard number to a variable. thanks, brooke
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v248 preview

• lines changed: 21181
• files changed: 163