CVS changes by file

review to branch (2010-03-30 to 2010-04-06) v228

• java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java
  • 1.14 lines changed: 19, context: html, text, full: html, text
    Made TrackCheck output much less verbose, changed links printed to be the same as those that produce the error, added the props file information to the first of the TrackCheck output, and removed some extra commented-out lines.
• java/src/edu/ucsc/genome/qa/lib/HgTracks.java
  • 1.19 lines changed: 6, context: html, text, full: html, text
    Made TrackCheck output much less verbose, changed links printed to be the same as those that produce the error, added the props file information to the first of the TrackCheck output, and removed some extra commented-out lines.
• java/src/edu/ucsc/genome/qa/lib/TestTarget.java
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Added a toString function in order to print target information in TrackCheck output.
• src/hg/encode/DAFs/2.0/:n
  • 1.2 lines changed: 53, context: html, text, full: html, text
    Bogus file
• src/hg/encode/DAFs/2.0/ucDHg19Hist.daf
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Added a new DAF for UC Davis, Snyder lab
• src/hg/encode/encodeCharts/README
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Brief instructions
• src/hg/encode/encodeCharts/encodeChart.pl
  • 1.2 lines changed: 35, context: html, text, full: html, text
    Added functionality to include important dates plus added some comments to code
  • 1.1 lines changed: 113, context: html, text, full: html, text
    Initial checkin
• src/hg/encode/encodeCharts/important.dates.tab
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Tab delimited file of important dates
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.32 lines changed: 11, context: html, text, full: html, text
    Added option to specify which metaTbl to use
• src/hg/encode/encodeMkChangeNotes/README
  • 1.1 lines changed: 48, context: html, text, full: html, text
    added more usage message and README
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • 1.8 lines changed: 1, context: html, text, full: html, text
    added pairedTagAlign file type
  • 1.7 lines changed: 1, context: html, text, full: html, text
    added csfasta file type
  • 1.6 lines changed: 1, context: html, text, full: html, text
    added csqual file type
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added more usage message and README
  • 1.4 lines changed: 69, context: html, text, full: html, text
    incorporated QA suggestions
• src/hg/encode/encodeMkChangeNotes/makefile
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added csfasta file type
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.223 lines changed: 1, context: html, text, full: html, text
    Revised the description of the UC Davis input, according to a request from the UC Davis folks
  • 1.222 lines changed: 6, context: html, text, full: html, text
    add 20k fragment size
  • 1.221 lines changed: 26, context: html, text, full: html, text
    Added two antibodies: ELK4 and IRF-1.
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.29 lines changed: 10, context: html, text, full: html, text
    Added stanzas to indicate that the term and tag fields are required in the cv file.
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.16 lines changed: 20, context: html, text, full: html, text
    Add assembly to reports
• src/hg/encode/encodeValidate/doReport.csh
  • 1.2 lines changed: 26, context: html, text, full: html, text
    Add assembly to reports
• src/hg/encode/encodeValidate/manual.all.txt
  • 1.2 lines changed: 21, context: html, text, full: html, text
    Add assembly to reports
• src/hg/encode/validateFiles/validateFiles.c
  • 1.39 lines changed: 2, context: html, text, full: html, text
    oops, remove BAM from the usage message if USE_BAM not defined
  • 1.38 lines changed: 20, context: html, text, full: html, text
    make BAM testing conditional on USE_BAM
• src/hg/hgTables/bedList.c
  • 1.71 lines changed: 2, context: html, text, full: html, text
    fix broken indentation that made code hard to read
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.518 lines changed: 1, context: html, text, full: html, text
    hgTrackUi.c
• src/hg/hgTracks/cds.h
  • 1.24 lines changed: 3, context: html, text, full: html, text
    Make the blue for query-insertion-at-end darker and bluer, so it is more easy to distinguish from the green for polyA.
• src/hg/hgTracks/hgTracks.c
  • 1.1636 lines changed: 9, context: html, text, full: html, text
    allow oryCun2 to find equivalent Ensembl scaffold names for blue bar
• src/hg/hgTracks/simpleTracks.c
  • 1.130 lines changed: 3, context: html, text, full: html, text
    If label area width exceeds 1/2 of image width, set to 1/2 of width instead of default.
• src/hg/hgTracks/wigTrack.c
  • 1.102 lines changed: 6, context: html, text, full: html, text
    Fix one last place where long strings in custom tracks cause problems
• src/hg/hgc/lowelab.c
  • 1.48 lines changed: 2, context: html, text, full: html, text
    change description for homologous gene track
• src/hg/hgc/mgcClick.c
  • 1.32 lines changed: 17, context: html, text, full: html, text
    improved description of MGC/RefSeq CDS similarity, fixed percent identity
• src/hg/inc/metaTbl.h
  • 1.9 lines changed: 9, context: html, text, full: html, text
    Eliminated call to obsolete metadataSetting(). Added support for NOT and wildcard in queries. Added support for setting multiple variables at once.
  • 1.8 lines changed: 17, context: html, text, full: html, text
    Reorganized and filled out metadataForTable routine
  • 1.7 lines changed: 40, context: html, text, full: html, text
    Tightening screws. Don't allow shared metaTbl update except from protected file.
  • 1.6 lines changed: 14, context: html, text, full: html, text
    Better handling of RA style files and extension to selection by 'vars'.
• src/hg/inc/trackDb.h
  • 1.55 lines changed: 14, context: html, text, full: html, text
    Added extras hash to the tdb struct and 2 APIs to use it
• src/hg/inc/versionInfo.h
  • 1.169 lines changed: 1, context: html, text, full: html, text
    "New version number v228"
• src/hg/js/hgTracks.js
  • 1.62 lines changed: 2, context: html, text, full: html, text
    change minchars to 2
• src/hg/lib/googleAnalytics.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Allow empty key to analyticsKey to disable google analytics (for overriding when one hg.conf includes another).
• src/hg/lib/hgFind.c
  • 1.226 lines changed: 2, context: html, text, full: html, text
    Fixed segv when an empty search term manages to make it to hgFind
• src/hg/lib/hui.c
  • 1.272 lines changed: 3, context: html, text, full: html, text
    backing out a change Tim made that breaks tracks without views
  • 1.271 lines changed: 2, context: html, text, full: html, text
    Oops, forgot an #ifdef USE_BAM (thanks Galt).
  • 1.270 lines changed: 47, context: html, text, full: html, text
    Round 2 of fixing 4-state checkbox lookup looking at both defaults and cart.
• src/hg/lib/metaTbl.c
  • 1.10 lines changed: 242, context: html, text, full: html, text
    Eliminated call to obsolete metadataSetting(). Added support for NOT and wildcard in queries. Added support for setting multiple variables at once.
  • 1.9 lines changed: 232, context: html, text, full: html, text
    Reorganized and filled out metadataForTable routine
  • 1.8 lines changed: 384, context: html, text, full: html, text
    Tightening screws. Don't allow shared metaTbl update except from protected file.
  • 1.7 lines changed: 233, context: html, text, full: html, text
    Better handling of RA style files and extension to selection by 'vars'.
• src/hg/lib/trackDbCustom.c
  • 1.82 lines changed: 30, context: html, text, full: html, text
    Added extras hash to the tdb struct and 2 APIs to use it
• src/hg/makeDb/doc/ailMel1.txt
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Adding BLASTZ, Chain/Net Support
  • 1.5 lines changed: 77, context: html, text, full: html, text
    Adding BLASTZ, Chain/Net support
• src/hg/makeDb/doc/bosTau4.txt
  • 1.23 lines changed: 59, context: html, text, full: html, text
    never got susScr1 to work finished with susScr2 lastz
• src/hg/makeDb/doc/calJac3.txt
  • 1.6 lines changed: 45, context: html, text, full: html, text
    adding ctgPos2 track
  • 1.5 lines changed: 557, context: html, text, full: html, text
    done and in the pushQ except for the multiz track
• src/hg/makeDb/doc/canFam2.txt
  • 1.30 lines changed: 38, context: html, text, full: html, text
    Adding LASTZ/Chain/Net support
• src/hg/makeDb/doc/danRer6.txt
  • 1.18 lines changed: 5, context: html, text, full: html, text
    added liftoverchain to danRer5
• src/hg/makeDb/doc/encodeDccHg18/openChromatinR3.notes.txt
  • 1.6 lines changed: 2, context: html, text, full: html, text
    changed typo of cap letters to lowercase in table and file for wgEncodeUncFAIREseqZinbaNhek
• src/hg/makeDb/doc/encodeDccHg18/uwDGF.release1.notes.txt
  • 1.1 lines changed: 97, context: html, text, full: html, text
    added UW DGF notes
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeGisRnaSeq.release1.notes.txt
  • 1.1 lines changed: 56, context: html, text, full: html, text
    notes... thanks Krish!
• src/hg/makeDb/doc/felCat3.txt
  • 1.56 lines changed: 14, context: html, text, full: html, text
    Remove grep 829.2 command
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.7 lines changed: 16, context: html, text, full: html, text
    Remove grep 829.2 command
  • 1.6 lines changed: 53, context: html, text, full: html, text
    Complete ctgPos2 track
  • 1.5 lines changed: 36, context: html, text, full: html, text
    Adding LASTZ/Chain/Net support
  • 1.4 lines changed: 108, context: html, text, full: html, text
    Adding LASTZ Chain/Net support
• src/hg/makeDb/doc/gorGor2.txt
  • 1.4 lines changed: 18, context: html, text, full: html, text
    have blat server and default location
• src/hg/makeDb/doc/hg16.txt
  • 1.12 lines changed: 14, context: html, text, full: html, text
    Regenerated kgTargetAli from knownGene table (instead of wrong build dir), but didn't reload -- Ann and I feel it's not worth the QA effort.
• src/hg/makeDb/doc/hg17.txt
  • 1.127 lines changed: 17, context: html, text, full: html, text
    DGV: data update (v9).
• src/hg/makeDb/doc/hg18.txt
  • 1.411 lines changed: 9, context: html, text, full: html, text
    Data update for gwasCatalog.
  • 1.410 lines changed: 1, context: html, text, full: html, text
    Remove grep 829.2 command
  • 1.409 lines changed: 16, context: html, text, full: html, text
    DGV: data update (v9).
  • 1.408 lines changed: 1, context: html, text, full: html, text
    Removed a line commented out.
  • 1.407 lines changed: 46, context: html, text, full: html, text
    Updated snpArrayIllumina HumanCytoSNP-12 SUB-TRACK.
• src/hg/makeDb/doc/hg19.txt
  • 1.95 lines changed: 6, context: html, text, full: html, text
    Data update for gwasCatalog.
  • 1.94 lines changed: 107, context: html, text, full: html, text
    DGV v9 (first time DGV is in hg19). Also a bit more info about how Belinda mapped over the personal genome variants track from hg18.
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.15 lines changed: 443, context: html, text, full: html, text
    first set of v57 done
• src/hg/makeDb/doc/mm9.txt
  • 1.132 lines changed: 17, context: html, text, full: html, text
    Documented replacing a mapability file with new data file due to missing data.
• src/hg/makeDb/doc/oryCun2.txt
  • 1.7 lines changed: 30, context: html, text, full: html, text
    ensGene v57 added and in the pushQ
• src/hg/makeDb/doc/oviAri1.txt
  • 1.1 lines changed: 664, context: html, text, full: html, text
    Initial oviAri1
• src/hg/makeDb/doc/rn4.txt
  • 1.40 lines changed: 11, context: html, text, full: html, text
    done with Panda ailMel1 lastz
• src/hg/makeDb/doc/susScr2.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Remove grep 829.2 command
  • 1.3 lines changed: 231, context: html, text, full: html, text
    susScr2 done and in the pushQ
• src/hg/makeDb/doc/uniProt/sp100331.txt
  • 1.1 lines changed: 50, context: html, text, full: html, text
    Added a new lightly-edited version of sp090821.txt, for fetching a fresh copy of UniProt and updating the appropriate files & tables.
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.114 lines changed: 1, context: html, text, full: html, text
    Added susScr2 - Pig
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.367 lines changed: 14, context: html, text, full: html, text
    Added oviAri1
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.106 lines changed: 1, context: html, text, full: html, text
    adding susScr2 to genbank updates on beta
  • 1.105 lines changed: 1, context: html, text, full: html, text
    adding panda
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.118 lines changed: 1, context: html, text, full: html, text
    Added susScr2 - Pig
• src/hg/makeDb/metaTblUpdate/metaTblPrint.c
  • 1.7 lines changed: 25, context: html, text, full: html, text
    Reworked usage(). Support ofr wildcard and NOT in selecting objects
  • 1.6 lines changed: 11, context: html, text, full: html, text
    Discover metaTbl name if not provided. Prefer sandBox version.
  • 1.5 lines changed: 36, context: html, text, full: html, text
    Better handling of RA style files and extension to select by 'vars'.
• src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
  • 1.9 lines changed: 88, context: html, text, full: html, text
    Added support for setting multiple vars from command line. Reworked usage(). Support ofr wildcard and NOT in selecting objects
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Oops. Changed objName to obj.
  • 1.7 lines changed: 90, context: html, text, full: html, text
    Tightening screws. Don't allow shared metaTbl update except from protected file.
  • 1.6 lines changed: 102, context: html, text, full: html, text
    Better handling of RA style files and extension to select by 'vars'.
• src/hg/makeDb/schema/all.joiner
  • 1.777 lines changed: 1, context: html, text, full: html, text
    further drift of the static mrnaID from the updated refLink table
  • 1.776 lines changed: 30, context: html, text, full: html, text
    adding susScr2 ailMel1 and fixing up chain checks
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • 1.41 lines changed: 5, context: html, text, full: html, text
    add verbose output to table check to find out who, what, why, where, when
• src/hg/makeDb/trackDb/cat/felCatV17e/description.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/cat/felCatV17e/trackDb.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Add Scaffolds ctgPos2 track
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • 1.11 lines changed: 9, context: html, text, full: html, text
    fixing some release alpha issues
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.939 lines changed: 453, context: html, text, full: html, text
    changed release beta,public to release public and release alpha to release alpha,beta for wgEncodeYaleChIPseq
  • 1.938 lines changed: 1639, context: html, text, full: html, text
    removed the entire release public block/sub-blocks for Open Chromatin and removed the release lines from the release alpha,beta blocks of Open Chromatin in preparation to release Open Chromatin (release 3) to the RR
  • 1.937 lines changed: 1, context: html, text, full: html, text
    changed default visibility of the Peaks (Zinba) to pack instead of hide. Planning to change back to hide once the v228 CGIs are released with a bug fix
  • 1.936 lines changed: 1, context: html, text, full: html, text
    Make that (Zinba)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.33 lines changed: 3, context: html, text, full: html, text
    Spelling mistakes and inconsistencies, oh my.
  • 1.32 lines changed: 7, context: html, text, full: html, text
    Zinba should also be in the release notes
  • 1.31 lines changed: 9, context: html, text, full: html, text
    Added description of Zinba peaks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • 1.6 lines changed: 8, context: html, text, full: html, text
    some edits from GIS
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.9 lines changed: 84, context: html, text, full: html, text
    some edits from GIS
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.5 lines changed: 8, context: html, text, full: html, text
    take out empty sections
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • 1.6 lines changed: 16, context: html, text, full: html, text
    make long labels fit 80 char limit
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    moving danRer5 shortLabel overrides from trackDb.ra into trackDb.chainNet.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.107 lines changed: 6, context: html, text, full: html, text
    moving danRer5 shortLabel overrides from trackDb.ra into trackDb.chainNet.ra
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.39 lines changed: 2, context: html, text, full: html, text
    Changing the panTro1 chain and net shortLabel overrides to really match the chainNet override.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.528 lines changed: 22, context: html, text, full: html, text
    changing default displays of burge tracks
• src/hg/makeDb/trackDb/knownAlt.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Clarifying altPromoter description in response to mailing list query.
• src/hg/makeDb/trackDb/makefile
  • 1.288 lines changed: 1, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/marmoset/calJac3/ctgPos2.html
  • 1.1 lines changed: 16, context: html, text, full: html, text
    now showing scaffold names
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.11 lines changed: 7, context: html, text, full: html, text
    added chain/net overrides for shortLabel for tetNig1 and tetNig2
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.36 lines changed: 6, context: html, text, full: html, text
    adding chain/net overrides for danRer5 on mouse (only affects mm9)
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • 1.4 lines changed: 14, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/panda/ailMel1/gap.html
  • 1.2 lines changed: 47, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/panda/ailMel1/gold.html
  • 1.2 lines changed: 8, context: html, text, full: html, text
    finalizing these document pages
• src/hg/makeDb/trackDb/pig/susScr2/bosTau4ChainPileUp.html
  • 1.3 lines changed: 7, context: html, text, full: html, text
    escaping the dollar signs in the html and the backslashes
  • 1.2 lines changed: 7, context: html, text, full: html, text
    can not use shell dollar sign strings in our html files
  • 1.1 lines changed: 50, context: html, text, full: html, text
    adding bosTau4ChainPileUp track
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • 1.4 lines changed: 2, context: html, text, full: html, text
    escaping the dollar signs in the html and the backslashes
  • 1.3 lines changed: 31, context: html, text, full: html, text
    add wiggle and bedGraph formats for comparison
  • 1.2 lines changed: 7, context: html, text, full: html, text
    adding bosTau4ChainPileUp track
• src/hg/makeDb/trackDb/rabbit/oryCun2/gap.html
  • 1.2 lines changed: 43, context: html, text, full: html, text
    finalizing gap,gold descriptions
• src/hg/makeDb/trackDb/rabbit/oryCun2/gold.html
  • 1.2 lines changed: 10, context: html, text, full: html, text
    finalizing gap,gold descriptions
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Correct project id
  • 1.1 lines changed: 128, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/sheep/oviAri1/gap.html
  • 1.1 lines changed: 30, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/sheep/oviAri1/gold.html
  • 1.1 lines changed: 34, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/sheep/oviAri1/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Initial oviAri1 support
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    removing unnecessary override
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.88 lines changed: 1, context: html, text, full: html, text
    o_db is sufficient at this time for felCatV17e
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.44 lines changed: 2, context: html, text, full: html, text
    Added release beta,public to chainCb3 and netCb3 to make them work with the non-composite versions at the worm level.
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.23 lines changed: 50, context: html, text, full: html, text
    ftp directories have underscore not period for separator
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Ensembl calJac3 is not our calJac3
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • 1.24 lines changed: 3, context: html, text, full: html, text
    need quotes around a string in a SQL insert statement
• src/hg/utils/phyloTrees/49way.dissect.txt
  • 1.1 lines changed: 679, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/49way.nh
  • 1.1 lines changed: 23, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/chainNet.pl
  • 1.5 lines changed: 7, context: html, text, full: html, text
    adding Sheep OviAra to a 49-way tree
• src/hg/utils/phyloTrees/placentals.txt
  • 1.1 lines changed: 57, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/hg/utils/phyloTrees/primates.txt
  • 1.1 lines changed: 25, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/hg/utils/phyloTrees/vertebrates.txt
  • 1.1 lines changed: 30, context: html, text, full: html, text
    From NCBI taxonomy viewer, species name lists
• src/inc/common.h
  • 1.169 lines changed: 6, context: html, text, full: html, text
    fixed GCC portability issues
• src/inc/common.mk
  • 1.78 lines changed: 14, context: html, text, full: html, text
    Removed redundant 'ifeq(${VAR},) VAR=0' -- if that evals true then the subsequent 'ifeq(${VAR},1)' would fail anyway. Did a little indenting/nesting of related var checks.
• src/inc/verbose.h
  • 1.9 lines changed: 6, context: html, text, full: html, text
    fixed GCC portability issues
• src/lib/errCatch.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    fixed 3264bit portability issue the right way
• src/lib/font/README
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier10.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier12.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier14.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier18.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier24.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier34.c
  • 1.1 lines changed: 2162, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgCourier8.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica10.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica12.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica14.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica18.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica24.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica34.c
  • 1.1 lines changed: 2229, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelvetica8.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold10.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold12.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold14.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold18.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold24.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold34.c
  • 1.1 lines changed: 2271, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHelveticaBold8.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgHugeFont.c
  • 1.2 lines changed: 5395, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgSail8.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgSixhi6.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes10.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes12.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes14.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes18.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes24.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes34.c
  • 1.1 lines changed: 1963, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/font/mgTimes8.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/gemfont.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram.
• src/lib/gemfont.h
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/makefile
  • 1.159 lines changed: 6, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/pscmGfx.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Adding fixed 34 font. Testing and tweaking for postScript output.
• src/lib/verbose.c
  • 1.7 lines changed: 20, context: html, text, full: html, text
    fixed GCC portability issues
• src/product/scripts/README
  • 1.3 lines changed: 2, context: html, text, full: html, text
    adding printEnv.pl
• src/product/scripts/printEnv.pl
  • 1.1 lines changed: 25, context: html, text, full: html, text
    initial source
• src/shortReads/i16Find/i16Find.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/i16Make/i16Make.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/itsaFind/itsaFind.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/itsaMake/itsaMake.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/splat/splat.c
  • 1.32 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/splatTestSet/splatTestSet.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/shortReads/splatToEland/splatToEland.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Backed out previous commit, as NULL has special meaning. Need to find a different solution for version of GCC that complain about NULL format string.
  • 1.23 lines changed: 1, context: html, text, full: html, text
    fixed invalid format in verbose call
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.22 lines changed: 1, context: html, text, full: html, text
    fixed GCC portability issues
• src/utils/qa/countRows.csh
  • 1.13 lines changed: 3, context: html, text, full: html, text
    changing usage statment and redirecting errors to stderr
• src/utils/qa/sessionStats.csh
  • 1.9 lines changed: 11, context: html, text, full: html, text
    added graph for users
  • 1.8 lines changed: 8, context: html, text, full: html, text
    added bar graph for number of sessions
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.107 lines changed: 3, context: html, text, full: html, text
    v228 final build

• lines changed: 23028
• files changed: 160