CVS changes by file

review to branch (2010-06-01 to 2010-06-07) v233

• src/README
  • 1.24 lines changed: 3, context: html, text, full: html, text
    Adding limit to line size.
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Updated daf to accept new dataTypes bigWig and bam. Updated, by request, Composite Name to seperate indvidual data types submitted by Open Chromatin.
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
  • 1.4 lines changed: 14, context: html, text, full: html, text
    take out fastq
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Added group type as this was accidently deleted previously.
• src/hg/encode/DAFs/2.0/sunyGeneST.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Took out ripAntibodies
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Updated daf to accept new dataTypes bigWig and bam. Updated, by request, Composite Name to seperate indvidual data types submitted by Open Chromatin.
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • 1.4 lines changed: 29, context: html, text, full: html, text
    Updated daf to accept new dataTypes bigWig and bam. Updated, by request, Composite Name to seperate indvidual data types submitted by Open Chromati, also changed name from UT -> UT-Austin
• src/hg/encode/DAFs/2.0/uwDnaseSeq.daf
  • 1.1 lines changed: 47, context: html, text, full: html, text
    First version of UW DnaseI HS daf
• src/hg/encode/encodeCharts/README
  • 1.4 lines changed: 54, context: html, text, full: html, text
    Updated README with latest info
• src/hg/encode/encodeCharts/encodeChart.pl
  • 1.3 lines changed: 147, context: html, text, full: html, text
    Deleted encodeChart.pl
• src/hg/encode/encodeCharts/encodeDist.py
  • 1.1 lines changed: 169, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeDistUnrelease.py
  • 1.1 lines changed: 170, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeReport.py
  • 1.1 lines changed: 112, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeReportFilter.py
  • 1.1 lines changed: 101, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeReportLib.py
  • 1.1 lines changed: 215, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeStatus.py
  • 1.1 lines changed: 169, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/encodeTimeline.py
  • 1.4 lines changed: 161, context: html, text, full: html, text
    Initial check-in of ENCODE Report Charts cgis
• src/hg/encode/encodeCharts/important.dates.tab
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Updated June 2010 freeze date
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • 1.6 lines changed: 5, context: html, text, full: html, text
    added some tool under dev'ment to deal with exp table
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.254 lines changed: 34, context: html, text, full: html, text
    Put them in order.
  • 1.253 lines changed: 34, context: html, text, full: html, text
    Added 2 approved cell lines for HAIB
  • 1.252 lines changed: 8, context: html, text, full: html, text
    dded ripInput to the ripTgtProtien table
  • 1.251 lines changed: 7, context: html, text, full: html, text
    Removed the duplicate 'None' term from ripTgtProtein
  • 1.250 lines changed: 1, context: html, text, full: html, text
    For term AP-2gamma: changed santibodyDescription -> antibodyDescription to be consistent with all other entries
  • 1.249 lines changed: 75, context: html, text, full: html, text
    Added mouse vocabularies including sex and age
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.33 lines changed: 5, context: html, text, full: html, text
    Added rank for UW
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.17 lines changed: 5, context: html, text, full: html, text
    UCD synonym doesn't help reporting so removing
  • 1.16 lines changed: 33, context: html, text, full: html, text
    Retiring wrangler emails. Adding synonymous labname for Farnham
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.231 lines changed: 1, context: html, text, full: html, text
    Added rank for UW
  • 1.230 lines changed: 1, context: html, text, full: html, text
    Allow ripTgtProtein to accept control terms, specifically 'None'.
• src/hg/encode/expTblTools/loadCVTbl
  • 1.2 lines changed: 46, context: html, text, full: html, text
    Updated schema to support types Antibody, protocol, control, treatment
  • 1.1 lines changed: 327, context: html, text, full: html, text
    added some tool under dev'ment to deal with exp table
• src/hg/hgGene/altSplice.c
  • 1.14 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgGenome/mainPage.c
  • 1.29 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgTables/bedList.c
  • 1.75 lines changed: 3, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/bigWig.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/compositeTrack.c
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/correlate.c
  • 1.81 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/correlatePlot.c
  • 1.18 lines changed: 17, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgTables/filterFields.c
  • 1.82 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/hgTables.h
  • 1.147 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/intersect.c
  • 1.54 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/mainPage.c
  • 1.154 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/schema.c
  • 1.66 lines changed: 12, context: html, text, full: html, text
    For bigWig and BAM, provide link to format/info.
• src/hg/hgTables/sumStats.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTables/wiggle.c
  • 1.79 lines changed: 2, context: html, text, full: html, text
    Fixing symbol conflict with table browser isBigWig function and new library function.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.527 lines changed: 3, context: html, text, full: html, text
    DGV: don't second-guess user filtering by include and deselecting all items.
  • 1.526 lines changed: 10, context: html, text, full: html, text
    Improvements to SNP controls' explanatory text -- thanks Mary!
• src/hg/hgTracks/coverageTrack.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgTracks/hgTracks.c
  • 1.1650 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgTracks/multiWig.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgTracks/searchTracks.c
  • 1.9 lines changed: 73, context: html, text, full: html, text
    support simple and advanced tabs
• src/hg/hgTracks/simpleTracks.c
  • 1.149 lines changed: 4, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
  • 1.148 lines changed: 3, context: html, text, full: html, text
    loadDgv: don't skip filtering when filterPmIds is NULL -- if the user has deselected everything but wants the filter to be include, we do need to filter.
  • 1.147 lines changed: 1, context: html, text, full: html, text
    Adding a few pixels to left label area so that it really does fit the number of characters you select.
  • 1.146 lines changed: 16, context: html, text, full: html, text
    Changed sprintf to safef for DECIPHER track.
• src/hg/hgTracks/variation.c
  • 1.148 lines changed: 1, context: html, text, full: html, text
    Comment tweak.
• src/hg/hgc/hgc.c
  • 1.1637 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/hgsqlTableDate/hgsqlTableDate.c
  • 1.1 lines changed: 50, context: html, text, full: html, text
    a utility to touch a file with the date of an SQL table (for use in a makefile)
• src/hg/hgsqlTableDate/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a utility to touch a file with the date of an SQL table (for use in a makefile)
• src/hg/inc/hvGfx.h
  • 1.6 lines changed: 12, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/inc/jksql.h
  • 1.89 lines changed: 1, context: html, text, full: html, text
    Changing return type of modification-date-ascertaining functions to time_t.
• src/hg/inc/versionInfo.h
  • 1.174 lines changed: 1, context: html, text, full: html, text
    "New version number v233"
• src/hg/instinct/hgBamBam/drawingCode.c
  • 1.8 lines changed: 6, context: html, text, full: html, text
    minor changes
• src/hg/instinct/hgBamBam/hgAnnotations.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    fixed bug
  • 1.6 lines changed: 1, context: html, text, full: html, text
    minor changes
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.gray2009.ra
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Updated data
• src/hg/js/hui.js
  • 1.59 lines changed: 3, context: html, text, full: html, text
    Fixed excluded filterComp options bug and made sure subtrack counts are updated with filterComp +/- buttons.
  • 1.58 lines changed: 27, context: html, text, full: html, text
    Added support for checkAll/uncheckAll on filterComposites.
• src/hg/js/ui.dropdownchecklist.js
  • 1.10 lines changed: 22, context: html, text, full: html, text
    Added support for checkAll/uncheckAll
• src/hg/js/utils.js
  • 1.31 lines changed: 114, context: html, text, full: html, text
    Added useful waitOnFinction() routine that makes sure wait cursor is seen.
• src/hg/lib/chromGraphFactory.c
  • 1.19 lines changed: 1, context: html, text, full: html, text
    adding some more search tables before we actually run off the end
• src/hg/lib/hui.c
  • 1.297 lines changed: 150, context: html, text, full: html, text
    Added All plus/minus buttons for filterComposites and added link to cv terms in filterComp box.
• src/hg/lib/hvGfx.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/lib/jksql.c
  • 1.141 lines changed: 2, context: html, text, full: html, text
    Changing return type of modification-date-ascertaining functions to time_t.
• src/hg/lib/wigAsciiToBinary.c
  • 1.35 lines changed: 12, context: html, text, full: html, text
    Making wigEncode abort on second track it sees.
• src/hg/makeDb/doc/calJac3.txt
  • 1.15 lines changed: 301, context: html, text, full: html, text
    phastCons support
• src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt
  • 1.16 lines changed: 3, context: html, text, full: html, text
    added two more /gbdb files to the deprecated files list
  • 1.15 lines changed: 3, context: html, text, full: html, text
    added two gbdb files to deprecated list
  • 1.14 lines changed: 8, context: html, text, full: html, text
    adding missing /gbdb files to new files section
• src/hg/makeDb/doc/felCat4.txt
  • 1.1 lines changed: 1820, context: html, text, full: html, text
    BLASTZ/CHAIN/NET
• src/hg/makeDb/doc/hg18.txt
  • 1.422 lines changed: 10, context: html, text, full: html, text
    Updated gwasCatalog.
• src/hg/makeDb/doc/hg19.txt
  • 1.117 lines changed: 45, context: html, text, full: html, text
    Regenerated snp131Exceptions, and snp131OrthoPt2Rm2Pa2 which depends on the exceptions. Multiple alignments were flagged even when there were single alignments to a chrom and chrom_hap, which had the effect of excluding haplo regions (even on main chroms) from ortho alignments.
  • 1.116 lines changed: 9, context: html, text, full: html, text
    Updated gwasCatalog: both new catalog data, and use just-released snp131 instead of snp130.
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • 1.6 lines changed: 7, context: html, text, full: html, text
    added import of new tables from ncbi
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • 1.7 lines changed: 60, context: html, text, full: html, text
    added import of new tables from ncbi
• src/hg/makeDb/genbank/src/ccds/ncbiSql/convertCreateTables
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added import of new tables from ncbi
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • 1.6 lines changed: 57, context: html, text, full: html, text
    added import of new tables from ncbi
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • 1.7 lines changed: 55, context: html, text, full: html, text
    added import of new tables from ncbi
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.71 lines changed: 2, context: html, text, full: html, text
    Removing hideFirst option, which no longer does anything.
• src/hg/makeDb/schema/all.joiner
  • 1.808 lines changed: 56, context: html, text, full: html, text
    Added many entries per Antonio's request.
• src/hg/makeDb/trackDb/checkMetaDb
  • 1.1 lines changed: 58, context: html, text, full: html, text
    utilities to check to see if metaDb needs to be rebuilt, and do so if necessary
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • 1.1 lines changed: 28, context: html, text, full: html, text
    utilities to check to see if metaDb needs to be rebuilt, and do so if necessary
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • 1.1 lines changed: 5, context: html, text, full: html, text
    Not sure if Yale should be in beta since it is identical in public and alpha. HAIB should be in beta.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaChipSeq.ra
  • 1.1 lines changed: 16571, context: html, text, full: html, text
    Not sure if Yale should be in beta since it is identical in public and alpha. HAIB should be in beta.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 24601, context: html, text, full: html, text
    Not sure if Yale should be in beta since it is identical in public and alpha. HAIB should be in beta.
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • 1.1 lines changed: 4, context: html, text, full: html, text
    Establishing the first publicly release mdb RA file
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleChIPseq.ra
  • 1.1 lines changed: 24601, context: html, text, full: html, text
    Establishing the first publicly release mdb RA file
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • 1.17 lines changed: 7, context: html, text, full: html, text
    changing calJac1 chain/nets so that they are for most dbs and for hg18, ornAna1 and monDom4
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.1003 lines changed: 2, context: html, text, full: html, text
    Shortening some long labels
  • 1.1002 lines changed: 166, context: html, text, full: html, text
    removed release alpha, beta tags and release public block in preparation for the mapability track release
  • 1.1001 lines changed: 1, context: html, text, full: html, text
    move HudsonAlphaRnaSeq to correct position
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    corrected some typos
  • 1.14 lines changed: 4, context: html, text, full: html, text
    add release notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    typo
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    move accession's to labVersion
  • 1.3 lines changed: 80, context: html, text, full: html, text
    removing release tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • 1.4 lines changed: 361, context: html, text, full: html, text
    changed release alpha to release alpha,beta to stage on hgwbeta
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Reverting to old matrix as promised
  • 1.2 lines changed: 587, context: html, text, full: html, text
    Shortened some offending shortLabels and longLabels to make Katrina happy
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
  • 1.2 lines changed: 41, context: html, text, full: html, text
    changed release beta,public to release public to stage on hgwbeta
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.alpha.ra
  • 1.7 lines changed: 145, context: html, text, full: html, text
    moving this track into the proper place
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
  • 1.3 lines changed: 18, context: html, text, full: html, text
    add addresses for rami, flo, and tim
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra
  • 1.1 lines changed: 141, context: html, text, full: html, text
    put this track in its proper place
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • 1.1 lines changed: 24, context: html, text, full: html, text
    Starting on description page for ENCODE regulatory supertrack.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • 1.1 lines changed: 7, context: html, text, full: html, text
    add makefile
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.123 lines changed: 1, context: html, text, full: html, text
    releasing snp131 take 2: removing release tags and changing visibility of snp130 to be hide by default
  • 1.122 lines changed: 6, context: html, text, full: html, text
    changing trackDb so that primate chain/nets have calJac3 rather than calJac1
  • 1.121 lines changed: 1, context: html, text, full: html, text
    backing snp131 off the RR to check possibly missing data
  • 1.120 lines changed: 4, context: html, text, full: html, text
    Updated gwasCatalog: both new catalog data, and use just-released snp131 instead of snp130.
  • 1.119 lines changed: 1, context: html, text, full: html, text
    making snp130 on hide by default so the coolness of snp131 can show through unhindered
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • 1.19 lines changed: 5, context: html, text, full: html, text
    include trackDb.wgEncodeSuny.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSuny.ra
  • 1.1 lines changed: 174, context: html, text, full: html, text
    This is a new track DB to hold the stuff from SunyAlbany
• src/hg/makeDb/trackDb/makeMetaDb
  • 1.3 lines changed: 18, context: html, text, full: html, text
    check dates before rebuilding metaDb
  • 1.2 lines changed: 5, context: html, text, full: html, text
    D'oh! check for no metaDb directory
  • 1.1 lines changed: 64, context: html, text, full: html, text
    make the metaDb table
• src/hg/makeDb/trackDb/makefile
  • 1.291 lines changed: 4, context: html, text, full: html, text
    check dates before rebuilding metaDb
  • 1.290 lines changed: 4, context: html, text, full: html, text
    added the build of metaDb
• src/hg/makeDb/trackDb/makefile.metaDb
  • 1.1 lines changed: 3, context: html, text, full: html, text
    utilities to check to see if metaDb needs to be rebuilt, and do so if necessary
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.15 lines changed: 3, context: html, text, full: html, text
    13-way phastCons
  • 1.14 lines changed: 11, context: html, text, full: html, text
    13-way phastCons
  • 1.13 lines changed: 8, context: html, text, full: html, text
    13-way phastCons
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • 1.1 lines changed: 6, context: html, text, full: html, text
    add for mm9
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
  • 1.13 lines changed: 9, context: html, text, full: html, text
    changing calJac1 chain/nets so that they are for most dbs and for hg18, ornAna1 and monDom4
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • 1.14 lines changed: 7, context: html, text, full: html, text
    changing calJac1 chain/nets so that they are for most dbs and for hg18, ornAna1 and monDom4
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.95 lines changed: 3, context: html, text, full: html, text
    changing calJac1 chain/nets so that they are for most dbs and for hg18, ornAna1 and monDom4
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.640 lines changed: 1, context: html, text, full: html, text
    releasing snp131 take 2: removing release tags and changing visibility of snp130 to be hide by default
  • 1.639 lines changed: 1, context: html, text, full: html, text
    backing snp131 off the RR to check possibly missing data
• src/hg/protein/lib/doTracks.c
  • 1.24 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/protein/pbGlobal/pbGlobal.c
  • 1.48 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/protein/pbTracks/pbTracks.c
  • 1.60 lines changed: 5, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • 1.12 lines changed: 46, context: html, text, full: html, text
    Fixed detection of multiple mappings to handle chr*_hap correctly, e.g. if a SNP maps to one chr6 pos and one chr6_cox_hap2 pos it is not multiply mapped. Other misc changes to accomodate human snp131.
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Make a track ixIxx file for the given to be used in the track search tool
• src/hg/utils/makeTrackIndex/makefile
  • 1.1 lines changed: 16, context: html, text, full: html, text
    Make a track ixIxx file for the given to be used in the track search tool
• src/hg/utils/makefile
  • 1.21 lines changed: 2, context: html, text, full: html, text
    add makeTrackIndex
• src/inc/bigWig.h
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Adding isBigWig function.
• src/inc/common.h
  • 1.174 lines changed: 4, context: html, text, full: html, text
    Added skipBeyondDelimit()
• src/inc/common.mk
  • 1.81 lines changed: 3, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/inc/memgfx.h
  • 1.30 lines changed: 48, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/inc/metaWig.h
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Removing parameter to metaWigOpen.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Removing bbiInternal include.
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Moving metaWig stuff from wigCorrelate to library.
• src/inc/portable.h
  • 1.31 lines changed: 1, context: html, text, full: html, text
    Changing return type of modification-date-ascertaining functions to time_t.
• src/inc/vGfx.h
  • 1.16 lines changed: 13, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/bwgCreate.c
  • 1.26 lines changed: 13, context: html, text, full: html, text
    ignore initial browser and track lines
• src/lib/bwgQuery.c
  • 1.24 lines changed: 13, context: html, text, full: html, text
    Adding isBigWig function.
• src/lib/cheapcgi.c
  • 1.136 lines changed: 2, context: html, text, full: html, text
    Added waitMask and inOutButton css classes
• src/lib/common.c
  • 1.151 lines changed: 21, context: html, text, full: html, text
    Added skipBeyondDelimit()
• src/lib/gifwrite.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/makefile
  • 1.160 lines changed: 4, context: html, text, full: html, text
    Moving metaWig stuff from wigCorrelate to library.
• src/lib/memgfx.c
  • 1.54 lines changed: 150, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/metaWig.c
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Removing parameter to metaWigOpen.
  • 1.1 lines changed: 184, context: html, text, full: html, text
    Moving metaWig stuff from wigCorrelate to library.
• src/lib/osunix.c
  • 1.48 lines changed: 1, context: html, text, full: html, text
    Changing return type of modification-date-ascertaining functions to time_t.
• src/lib/pngwrite.c
  • 1.4 lines changed: 8, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/pscmGfx.c
  • 1.29 lines changed: 2, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/vGfxPrivate.h
  • 1.11 lines changed: 2, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/lib/vGif.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    add support for 32-bit color (make USE_PNG have global consequence)
• src/utils/gitTools/gitFiles
  • 1.1 lines changed: 22, context: html, text, full: html, text
    adding first gitTools
• src/utils/gitTools/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    adding first gitTools
• src/utils/makefile
  • 1.78 lines changed: 1, context: html, text, full: html, text
    Adding wigCorrelate to build.
  • 1.77 lines changed: 2, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/makefile
  • 1.1 lines changed: 22, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c
  • 1.1 lines changed: 131, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/expected/qSubRangeTest.psl
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/expected/qtSubRangeTest.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/expected/tSubRangeTest.psl
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/qSubrange.psl
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/qSubrange.qsizes
  • 1.1 lines changed: 1, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.qsizes
  • 1.1 lines changed: 1, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.sizes
  • 1.1 lines changed: 2, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/tSubrange.psl
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/input/tSubrange.tsizes
  • 1.1 lines changed: 1, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/pslLiftSubrangeBlat/tests/makefile
  • 1.1 lines changed: 28, context: html, text, full: html, text
    added program to lift blat subrange queries
• src/utils/qa/findBrokenLinks.csh
  • 1.1 lines changed: 10, context: html, text, full: html, text
    This has been used in cron jobs run by Angie to find broken links in gbdb and goldenPath for a long time. The jobs are switching to the qateam crontab, and we are finally checking this little script in.
• src/utils/qa/makefile
  • 1.124 lines changed: 4, context: html, text, full: html, text
    Added findBrokenLinks.csh and a comment about how to install in /cluster/bin/scripts since Hiram changed the SCRIPTS defined in common.mk.
• src/utils/qa/qaEncodeTracks.csh
  • 1.14 lines changed: 3, context: html, text, full: html, text
    changed max shortLabel to 17 characters
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.118 lines changed: 3, context: html, text, full: html, text
    v233 final build
• src/utils/wigCorrelate/wigCorrelate.c
  • 1.7 lines changed: 27, context: html, text, full: html, text
    Removing parameter to metaWigOpen.
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Fixing includes so compiles again.
  • 1.5 lines changed: 209, context: html, text, full: html, text
    Moving metaWig stuff from wigCorrelate to library.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed typo in comment.
• src/utils/wigToBed/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work.
• src/utils/wigToBed/wigToBed.c
  • 1.1 lines changed: 95, context: html, text, full: html, text
    Seems to work.

• lines changed: 74206
• files changed: 155