CVS changes by file

branch to review (2010-03-23 to 2010-03-30) v228

• java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixing server location and dbs checked - an error introduced by me with my last commit.
• src/hg/encode/DAFs/2.0/affyRnaChip.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/broadMapability.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/buOrchid.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/cshlRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Cleaned up the composite and dataType suffixes
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/dukeExonArray.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/gisDnaPet.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/gisRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/haibMethylSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/haibRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/helicosRnaSeq.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/nhgriElnitskiBiPro.daf
  • 1.3 lines changed: 20, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/nhgriElnitskiNegReg.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Cleaned up the composite and dataType suffixes
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Initial check in of a subset of the stanford DAFs
• src/hg/encode/DAFs/2.0/stanfordRnaSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/sunyRipChip.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uMassWengTfbsValid.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Cleaned up the composite and dataType suffixes
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Add data agreement suffix
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Cleaned up the composite and dataType suffixes
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uwDnaseValid.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/DAFs/2.0/uwExonArray.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Add track group
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.31 lines changed: 9, context: html, text, full: html, text
    Fixed bug that prevented non-metaTbl metadata from showing up without special flag
  • 1.30 lines changed: 17, context: html, text, full: html, text
    Expanded to a near complet sort order list, added noMetaTbl option to compare old and new metadata methods, expanded fileMask to include bigWig, bigBed and BAM.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.75 lines changed: 49, context: html, text, full: html, text
    add bigWig
  • 1.74 lines changed: 29, context: html, text, full: html, text
    remove all README stuff
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.220 lines changed: 2, context: html, text, full: html, text
    Changed the sex of CH12 to U.
  • 1.219 lines changed: 14, context: html, text, full: html, text
    Re-added CH12
  • 1.218 lines changed: 0, context: html, text, full: html, text
    Adding CH12, provisionally
  • 1.217 lines changed: 103, context: html, text, full: html, text
    Added missing JunD description and antibody validation document variable
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.15 lines changed: 11, context: html, text, full: html, text
    Minor changes
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.219 lines changed: 18, context: html, text, full: html, text
    add support for BAM download only
  • 1.218 lines changed: 21, context: html, text, full: html, text
    1. Allow control terms to be used with any variable 2. Add co-PI to lab metadata
  • 1.217 lines changed: 14, context: html, text, full: html, text
    1. Special handling of 'None' 2. Table/filename gen uses view and replicate last
  • 1.216 lines changed: 3, context: html, text, full: html, text
    Proper error if CV term is not registered
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Change to file/tablenaming conventions
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.12 lines changed: 3, context: html, text, full: html, text
    Change to file/tablenaming conventions
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.31 lines changed: 89, context: html, text, full: html, text
    Added link for antibody validation documents. Now if we can just get some.
• src/hg/encode/validateFiles/makefile
  • 1.5 lines changed: 4, context: html, text, full: html, text
    add a couple of tests for bigWig and BAM
• src/hg/encode/validateFiles/tests/test3.bam
  • 1.1 lines changed: 0, context: html, text, full: html, text
    a simple BAM test
• src/hg/encode/validateFiles/tests/test3.right.txt
  • 1.1 lines changed: 0, context: html, text, full: html, text
    a simple BAM test
• src/hg/encode/validateFiles/tests/test4.bw
  • 1.1 lines changed: 0, context: html, text, full: html, text
    a small test for bigWig
• src/hg/encode/validateFiles/tests/test4.right.txt
  • 1.1 lines changed: 0, context: html, text, full: html, text
    a small test for bigWig
• src/hg/encode/validateFiles/validateFiles.c
  • 1.37 lines changed: 12, context: html, text, full: html, text
    fix up some printf's and add flag allowing non-native chroms
• src/hg/hgGenome/bedList.c
  • 1.6 lines changed: 7, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgGenome/hgGenome.c
  • 1.66 lines changed: 1, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgGenome/hgGenome.h
  • 1.39 lines changed: 4, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgGenome/import.c
  • 1.17 lines changed: 42, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTables/bedList.c
  • 1.70 lines changed: 1, context: html, text, full: html, text
    don't free cached connection with sqlDisconnect
  • 1.69 lines changed: 3, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTables/custom.c
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTables/hgTables.c
  • 1.189 lines changed: 14, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTables/hgTables.h
  • 1.139 lines changed: 3, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTables/mainPage.c
  • 1.147 lines changed: 2, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.517 lines changed: 101, context: html, text, full: html, text
    Moving bam configuration code from hgTrackUi to hui to support bam in multi-view composites.
• src/hg/hgTracks/bedGraph.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTracks/bedTrack.c
  • 1.24 lines changed: 8, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTracks/bigBedTrack.c
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTracks/bigWigTrack.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgTracks/config.c
  • 1.91 lines changed: 2, context: html, text, full: html, text
    Adding additional font options to config page.
• src/hg/hgTracks/hgTracks.h
  • 1.203 lines changed: 2, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
  • 1.202 lines changed: 6, context: html, text, full: html, text
    Adding utility functions to get darker colors. Using one of these to darken text when primary color is too light.
• src/hg/hgTracks/simpleTracks.c
  • 1.129 lines changed: 37, context: html, text, full: html, text
    Adding utility functions to get darker colors. Using one of these to darken text when primary color is too light.
• src/hg/hgc/encodeClick.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Peaks and Points oh my
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Point peaks should be 1 based.
• src/hg/hgc/hgc.c
  • 1.1608 lines changed: 1, context: html, text, full: html, text
    DGV: when both thickEnd and thickStart are set to chromStart, as they are since we stopped showing locus whiskers, don't print out separate positions for variant vs. locus because there's only the variant now.
  • 1.1607 lines changed: 4, context: html, text, full: html, text
    Hook ikmc into komp code, for table name change requested by contributor Carol Bult.
  • 1.1606 lines changed: 1, context: html, text, full: html, text
    Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
• src/hg/hgsql/hgsql.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    make functionality match usage message by making the database optional on the command line
• src/hg/inc/hui.h
  • 1.147 lines changed: 3, context: html, text, full: html, text
    Moving bam configuration code from hgTrackUi to hui to support bam in multi-view composites.
• src/hg/inc/metaTbl.h
  • 1.5 lines changed: 19, context: html, text, full: html, text
    Some adjustments recommened by Mark in code review
• src/hg/inc/trackDb.h
  • 1.54 lines changed: 2, context: html, text, full: html, text
    Added an eCfgType for bam, to support bam in multi-view composites. (Should eCfgType be in hui instead of here?)
• src/hg/lib/hgFindSpecCustom.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    When filling in searchDescription using tdb->longLabel, just omit the table name because it is often more confusing than informative.
• src/hg/lib/hui.c
  • 1.269 lines changed: 0, context: html, text, full: html, text
    Adding additional font options to config page.
  • 1.268 lines changed: 5, context: html, text, full: html, text
    Fix to evaluating subtrackFourStateChecked checkBox
  • 1.267 lines changed: 3, context: html, text, full: html, text
    Handle slightly changed metaTbl API
  • 1.266 lines changed: 99, context: html, text, full: html, text
    Moving bam configuration code from hgTrackUi to hui to support bam in multi-view composites.
• src/hg/lib/metaTbl.c
  • 1.6 lines changed: 82, context: html, text, full: html, text
    Some adjustments recommened by Mark in code review
  • 1.5 lines changed: 26, context: html, text, full: html, text
    Check for metaTbl before querying.
• src/hg/lib/trackDbCustom.c
  • 1.81 lines changed: 2, context: html, text, full: html, text
    Added an eCfgType for bam, to support bam in multi-view composites. (Should eCfgType be in hui instead of here?)
• src/hg/lib/trackLayout.c
  • 1.4 lines changed: 79, context: html, text, full: html, text
    Adding additional font options to config page.
• src/hg/makeDb/doc/canFam2.txt
  • 1.29 lines changed: 53, context: html, text, full: html, text
    Adding felCatV17e BLASTZ/CHAIN/NET tracks
• src/hg/makeDb/doc/encodeDccHg18/openChromatinR3.notes.txt
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added one more Zinba peak
  • 1.4 lines changed: 26, context: html, text, full: html, text
    Last minute addition of Zinba peaks
• src/hg/makeDb/doc/hg18.txt
  • 1.406 lines changed: 400, context: html, text, full: html, text
    Some really old changes: snp130 func annotation fixes, hapmap and 1000 genomes experimental work (some interrupted).
• src/hg/makeDb/doc/hg19.txt
  • 1.93 lines changed: 68, context: html, text, full: html, text
    Adding felCatV17e BLASTZ/CHAIN/NET tracks
  • 1.92 lines changed: 48, context: html, text, full: html, text
    done with susScr2 lastz and swap
• src/hg/makeDb/doc/mm9.txt
  • 1.131 lines changed: 52, context: html, text, full: html, text
    Adding felCatV17e BLASTZ/CHAIN/NET tracks
  • 1.130 lines changed: 51, context: html, text, full: html, text
    done with susScr2 lastz and swap
  • 1.129 lines changed: 3, context: html, text, full: html, text
    Renamed komp to ikmc as requested by contributor Carol Bult.
• src/hg/makeDb/doc/monDom5.txt
  • 1.21 lines changed: 58, context: html, text, full: html, text
    Adding felCatV17e BLASTZ/CHAIN/NET tracks
  • 1.20 lines changed: 48, context: html, text, full: html, text
    done with susScr2 lastz and swap
• src/hg/makeDb/doc/susScr2.txt
  • 1.2 lines changed: 318, context: html, text, full: html, text
    running a bosTau4 lastz and done with swaps from hg19 mm9 and monDom5
  • 1.1 lines changed: 81, context: html, text, full: html, text
    initial browser up and running
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.366 lines changed: 14, context: html, text, full: html, text
    adding susScr2 - Pig
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.88 lines changed: 1, context: html, text, full: html, text
    Enabled genbank updates for elephant on RR.
• src/hg/makeDb/hgCalStat/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    prevent permission errors when installing scripts
• src/hg/makeDb/metaTblUpdate/metaTblPrint.c
  • 1.4 lines changed: 13, context: html, text, full: html, text
    Some adjustments recommended by Mark in code reivew
• src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
  • 1.5 lines changed: 10, context: html, text, full: html, text
    Some adjustments recommended by Mark in code reivew
• src/hg/makeDb/schema/all.joiner
  • 1.775 lines changed: 5, context: html, text, full: html, text
    Added ikmc (new name of komp).
• src/hg/makeDb/trackDb/README
  • 1.105 lines changed: 11, context: html, text, full: html, text
    Adding info on type factorSource.
• src/hg/makeDb/trackDb/anopheles/trackDb.ra
  • 1.21 lines changed: 40, context: html, text, full: html, text
    removing redundant stuff
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.22 lines changed: 10, context: html, text, full: html, text
    proper priorities on chainNetPoodle and RheMac2 and DanRer5
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Adding felCatV17e trackDb.chainNet
• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
  • 1.5 lines changed: 11, context: html, text, full: html, text
    Elephant release
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.935 lines changed: 25, context: html, text, full: html, text
    Added one Zinba peak and changed the view from Zinba Peaks to Peaks Zinba
  • 1.934 lines changed: 2, context: html, text, full: html, text
    Forgot to set dateResubmitted
  • 1.933 lines changed: 2, context: html, text, full: html, text
    Corrected metadata for 2 HAIB TFBS tracks that needed to be resubmitted
  • 1.932 lines changed: 3, context: html, text, full: html, text
    Zinba peaks have qValue and no pValue
  • 1.931 lines changed: 75, context: html, text, full: html, text
    Added Zinba peaks to FAIRE portion of Open Chrom
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.48 lines changed: 9, context: html, text, full: html, text
    Ready for release3
• src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    some small edits, addition of link to protocol
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.106 lines changed: 3, context: html, text, full: html, text
    moved ailent array lifts (from hg18) back to variation group
• src/hg/makeDb/trackDb/makefile
  • 1.287 lines changed: 2, context: html, text, full: html, text
    adding susScr2 to the build
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • 1.1 lines changed: 117, context: html, text, full: html, text
    Copying komp definitions to ikmc to support table rename requested by contributor (Carol Bult).
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.211 lines changed: 28, context: html, text, full: html, text
    Copying komp definitions to ikmc to support table rename requested by contributor (Carol Bult).
• src/hg/makeDb/trackDb/pig/susScr2/ctgPos2.html
  • 1.1 lines changed: 18, context: html, text, full: html, text
    adding ctgPos2 track
• src/hg/makeDb/trackDb/pig/susScr2/description.html
  • 1.2 lines changed: 36, context: html, text, full: html, text
    finishing off these description pages
  • 1.1 lines changed: 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr2/gap.html
  • 1.2 lines changed: 49, context: html, text, full: html, text
    finishing off these description pages
  • 1.1 lines changed: 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr2/gold.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    adding ctgPos2 track
  • 1.2 lines changed: 27, context: html, text, full: html, text
    finishing off these description pages
  • 1.1 lines changed: 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • 1.1 lines changed: 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/trackDb.ra
  • 1.2 lines changed: 7, context: html, text, full: html, text
    adding ctgPos2 track
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.87 lines changed: 51, context: html, text, full: html, text
    Adding felCatV17e trackDb.chainNet
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.80 lines changed: 31, context: html, text, full: html, text
    Removed alpha and beta,public from vegaGene and vegaPseudoGene tracks, as they contained the same info.
• src/hg/oneShot/freen/freen.c
  • 1.99 lines changed: 10, context: html, text, full: html, text
    Adding 14 point fonts and labeling bold.
  • 1.98 lines changed: 44, context: html, text, full: html, text
    Making freen put up a test image of fonts.
• src/hg/overlapSelect/selectTable.c
  • 1.32 lines changed: 2, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/idMatchSimple.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/idMatchSimpleNon.gp
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/psl_idMatch.drop.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/psl_idMatch.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/psl_idMatch_non.drop.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/expected/psl_idMatch_non.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/input/idMatchSimple1.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/input/idMatchSimple2.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/overlapSelect/tests/makefile
  • 1.36 lines changed: 10, context: html, text, full: html, text
    fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do
• src/hg/ratStuff/mafSpeciesSubset/makefile
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    making makefile ready for HG_APPLIST usage
• src/hg/ratStuff/mafsInRegion/makefile
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    every makefile should have a clean target
• src/hg/utils/automation/Encode.pm
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    add bigWig
• src/hg/utils/automation/EnsGeneAutomate.pm
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    adding version 57 definitions
• src/hg/utils/gapToLift/gapToLift.c
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    add minGap argument
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    clarified error handling
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    oops fixes 32bit error gff3ToGenePred.c:58: warning: cast from pointer to integer of different size make[3]:
• src/inc/memgfx.h
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    Adding a bunch of xfree fonts.
• src/lib/font/mgCourier10.c
  • 1.1 lines changed: 299, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgCourier12.c
  • 1.1 lines changed: 364, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgCourier14.c
  • 1.1 lines changed: 734, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgCourier18.c
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    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgCourier24.c
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    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgCourier8.c
  • 1.1 lines changed: 273, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica10.c
  • 1.1 lines changed: 335, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica12.c
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    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica14.c
  • 1.1 lines changed: 527, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica18.c
  • 1.1 lines changed: 845, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica24.c
  • 1.1 lines changed: 1245, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelvetica8.c
  • 1.1 lines changed: 278, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold10.c
  • 1.1 lines changed: 345, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold12.c
  • 1.1 lines changed: 424, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold14.c
  • 1.1 lines changed: 579, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold18.c
  • 1.1 lines changed: 883, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold24.c
  • 1.1 lines changed: 1277, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHelveticaBold8.c
  • 1.1 lines changed: 285, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgHugeFont.c
  • 1.1 lines changed: 5395, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgSail8.c
  • 1.1 lines changed: 112, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgSixhi6.c
  • 1.1 lines changed: 208, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes10.c
  • 1.1 lines changed: 324, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes12.c
  • 1.1 lines changed: 424, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes14.c
  • 1.1 lines changed: 500, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes18.c
  • 1.1 lines changed: 764, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes24.c
  • 1.1 lines changed: 1193, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/font/mgTimes8.c
  • 1.1 lines changed: 256, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/gemfont.c
  • 1.10 lines changed: 13, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/gemfont.h
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/makefile
  • 1.158 lines changed: 11, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/memgfx.c
  • 1.52 lines changed: 2, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/mgHugeFont.c
  • 1.6 lines changed: 5377, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/mgLargeFont.c
  • 1.6 lines changed: 2391, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/mgMediumFont.c
  • 1.6 lines changed: 1430, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/mgSmallFont.c
  • 1.5 lines changed: 709, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/mgTinyFont.c
  • 1.5 lines changed: 700, context: html, text, full: html, text
    Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it.
• src/lib/pipeline.c
  • 1.24 lines changed: 15, context: html, text, full: html, text
    readability changes suggest by Tim
• src/makefile
  • 1.71 lines changed: 1, context: html, text, full: html, text
    making makefile ready for HG_APPLIST usage
• src/utils/bdfToGem/bdfToGem.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Updating to include lineHeight.
  • 1.14 lines changed: 7, context: html, text, full: html, text
    Removing an extra free that was causing crash. Fixing some compiler warnings.
• src/utils/cvsTools/makefile
  • 1.5 lines changed: 2, context: html, text, full: html, text
    prevent permission errors when installing scripts
• src/utils/newProg/newProg.c
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    it is EXE not EXT
• src/utils/qa/countRows.csh
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    changed script so that can also check genome-mysql
• src/utils/qa/qaEncodeTracks.csh
  • 1.12 lines changed: 1, context: html, text, full: html, text
    changing tableCoord info
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.106 lines changed: 2, context: html, text, full: html, text
    v228 preview

• lines changed: 34624
• files changed: 174