CVS changes by file

branch to review (2009-11-10 to 2009-11-17) v220

• src/hg/encode/DAFs/YDHRnaSeq.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Minor change to validationSettings
• src/hg/encode/DAFs/YDHRnaSeqTreatment.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Minor change to validationSettings
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    continue to make Tim do most of the work (Bwahhh haha)
• src/hg/encode/validateFiles/validateFiles.c
  • 1.29 lines changed: 9, context: html, text, full: html, text
    validateFiles.c
• src/hg/hgTracks/bamTrack.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    bamDrawAt: Skip zero-length blocks or blocks out of the viewing window.
• src/hg/hgTracks/cds.c
  • 1.104 lines changed: 35, context: html, text, full: html, text
    bugfix: don't assume we have linkedFeatures in baseColorInitTrack because this is called for linkedFeaturesSeries too. Use tg->drawItems as a proxy for type (lf vs. lfs). Then the proper range is set and we can replace a slow hDnaFromSeq call with getCachedDna.
• src/hg/hgTracks/cds.h
  • 1.23 lines changed: 14, context: html, text, full: html, text
    bugfix: don't assume we have linkedFeatures in baseColorInitTrack because this is called for linkedFeaturesSeries too. Use tg->drawItems as a proxy for type (lf vs. lfs). Then the proper range is set and we can replace a slow hDnaFromSeq call with getCachedDna.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.19 lines changed: 4, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/config.c
  • 1.86 lines changed: 5, context: html, text, full: html, text
    Bob does not want no double negatives so I disabled the disable and instead enabled 'Enable advanced javascript features'
  • 1.85 lines changed: 7, context: html, text, full: html, text
    Changed 'Enable drag-zoom' to 'Disable advanced javascript features' in preparation for imageV2
• src/hg/hgTracks/expRatioTracks.c
  • 1.46 lines changed: 8, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/hgTracks.c
  • 1.1607 lines changed: 50, context: html, text, full: html, text
    Changes to fix no leftLabel bug and changes to support separate button slice (needed for subtracks with separate imgTracks)
  • 1.1606 lines changed: 3, context: html, text, full: html, text
    Changed 'Enable drag-zoom' to 'Disable advanced javascript features' in preparation for imageV2
  • 1.1605 lines changed: 65, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/hgTracks.h
  • 1.192 lines changed: 3, context: html, text, full: html, text
    Adding whisker plots.
  • 1.191 lines changed: 6, context: html, text, full: html, text
    bugfix: don't assume we have linkedFeatures in baseColorInitTrack because this is called for linkedFeaturesSeries too. Use tg->drawItems as a proxy for type (lf vs. lfs). Then the proper range is set and we can replace a slow hDnaFromSeq call with getCachedDna.
  • 1.190 lines changed: 1, context: html, text, full: html, text
    Changed 'Enable drag-zoom' to 'Disable advanced javascript features' in preparation for imageV2
• src/hg/hgTracks/imageV2.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Background color of image should only be red for debugging
  • 1.13 lines changed: 20, context: html, text, full: html, text
    Changes to fix no leftLabel bug and changes to support separate button slice (needed for subtracks with separate imgTracks)
  • 1.12 lines changed: 60, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/imageV2.h
  • 1.10 lines changed: 10, context: html, text, full: html, text
    Changes to fix no leftLabel bug and changes to support separate button slice (needed for subtracks with separate imgTracks)
  • 1.9 lines changed: 1, context: html, text, full: html, text
    FINALLY, checkin imageV2 framework without features.
  • 1.8 lines changed: 29, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/simpleTracks.c
  • 1.113 lines changed: 7, context: html, text, full: html, text
    Adding whisker plots.
  • 1.112 lines changed: 1, context: html, text, full: html, text
    bugfix: don't assume we have linkedFeatures in baseColorInitTrack because this is called for linkedFeaturesSeries too. Use tg->drawItems as a proxy for type (lf vs. lfs). Then the proper range is set and we can replace a slow hDnaFromSeq call with getCachedDna.
  • 1.111 lines changed: 33, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/variation.c
  • 1.145 lines changed: 8, context: html, text, full: html, text
    Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2
• src/hg/hgTracks/wigCommon.h
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/hgTracks/wigTrack.c
  • 1.96 lines changed: 14, context: html, text, full: html, text
    Making whiskers take light and medium color from primary color rather than always using grays.
  • 1.95 lines changed: 154, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/inc/hui.h
  • 1.142 lines changed: 4, context: html, text, full: html, text
    Adding whisker plots.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.12 lines changed: 565, context: html, text, full: html, text
    November 2009 data release update
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.21 lines changed: 40, context: html, text, full: html, text
    171819 data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.users.ra
  • 1.2 lines changed: 20, context: html, text, full: html, text
    
• src/hg/instinct/hgPathways/hgPathwaysFrontend/hgPathwayStyle.css
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Updated to handle second canvas to do movement with
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Added queuing system for ajax requests, and coordinate display mode
• src/hg/instinct/hgPathways/hgPathwaysFrontend/index.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Updated to handle second canvas to do movement with
  • 1.10 lines changed: 44, context: html, text, full: html, text
    Added queuing system for ajax requests, and coordinate display mode
• src/hg/instinct/hgPathways/hgPathwaysFrontend/js/hgHeatPath.js
  • 1.16 lines changed: 107, context: html, text, full: html, text
    Updated to handle second canvas to do movement with
  • 1.15 lines changed: 127, context: html, text, full: html, text
    Added queuing system for ajax requests, and coordinate display mode
• src/hg/instinct/mapProbesToGenes/mapProbesToGenes.c
  • 1.9 lines changed: 30, context: html, text, full: html, text
    Fix to prevent query from timing out if there's lots of probes
• src/hg/js/hgTracks.js
  • 1.45 lines changed: 19, context: html, text, full: html, text
    Change to support buttonSlice (code isn't even used without dragScroll which is disabled)
• src/hg/js/hui.js
  • 1.43 lines changed: 104, context: html, text, full: html, text
    Changes to allow the 5th dimension
• src/hg/js/utils.js
  • 1.25 lines changed: 20, context: html, text, full: html, text
    Added some obvious array functions
• src/hg/lib/hui.c
  • 1.249 lines changed: 3, context: html, text, full: html, text
    Adding whisker plots.
  • 1.248 lines changed: 13, context: html, text, full: html, text
    Fix uninitialized variables, which hit on matrix X no Y
  • 1.247 lines changed: 227, context: html, text, full: html, text
    Changes to allow the 5th dimension
• src/hg/lib/lsSnpPdbChimera.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    fixed incorrect code generation when no SNPs are mapped to structure
• src/hg/lib/wiggleCart.c
  • 1.26 lines changed: 297, context: html, text, full: html, text
    Refactored wigFetchMinMaxYWithCart. It is still quite complex because I kept the old behavior that tolerates missing data range specifications (although it does warn now). When hgTrackDb is enhanced to enforce data range specs, this can become a lot simpler -- but still not simple because we still allow the viewLimits setting (not defaultViewLimits) to push out the data range boundaries.
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Initializing some vars to zero to fix compiler warning on older compiler that wasn't quite sophisticated enough to see that these are actually initialized in all paths.
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.9 lines changed: 39, context: html, text, full: html, text
    Old... Broad into QA for release2
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • 1.10 lines changed: 448, context: html, text, full: html, text
    Finish with Base overloap and getting release2 into QA
• src/hg/makeDb/doc/encodeDccHg18/gencode.txt
  • 1.4 lines changed: 456, context: html, text, full: html, text
    Loaded version v3c
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.3 lines changed: 40, context: html, text, full: html, text
    Old stuff needing to be checked in
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.11 lines changed: 12, context: html, text, full: html, text
    Dribbling in
• src/hg/makeDb/doc/hg19.txt
  • 1.61 lines changed: 245, context: html, text, full: html, text
    done with hg19 46-way track, once again
• src/hg/makeDb/doc/susScr1.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    human proteins
  • 1.2 lines changed: 164, context: html, text, full: html, text
    started Human Proteins
  • 1.1 lines changed: 197, context: html, text, full: html, text
    Working on the genbank run
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.95 lines changed: 14, context: html, text, full: html, text
    
  • 1.94 lines changed: 25, context: html, text, full: html, text
    171819 data
• src/hg/makeDb/schema/all.joiner
  • 1.743 lines changed: 14, context: html, text, full: html, text
    added Burge RNA-seq data tables to list of tables to be ignored for hg.
• src/hg/makeDb/trackDb/README
  • 1.90 lines changed: 19, context: html, text, full: html, text
    Added instructions for the 'ABC' dimensions
• src/hg/makeDb/trackDb/chicken/bgiCov.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to Beijing Genomics Institute.
• src/hg/makeDb/trackDb/chicken/bgiSnp.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to Beijing Genomics Institute.
• src/hg/makeDb/trackDb/chicken/galGal2/bgiGene.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to Beijing Genomics Institute.
• src/hg/makeDb/trackDb/chicken/galGal2/bgiSnp.html
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to Beijing Genomics Institute.
• src/hg/makeDb/trackDb/human/hg18/burgeRnaSeqGemMapperAlign.html
  • 1.1 lines changed: 55, context: html, text, full: html, text
    Description page for Burge RNA-seq data re-mapped with GEM mapper.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.423 lines changed: 1, context: html, text, full: html, text
    changed Burge RNA-seq data track default visibility to hide.
  • 1.422 lines changed: 107, context: html, text, full: html, text
    added Burge lab data mapped using GEM mapper.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.659 lines changed: 67, context: html, text, full: html, text
    Added minLimit, maxLimit to bedGraph subtracks of wgEncodeGisPet from sql min & max queries on bedGraph tables missing those settings.
  • 1.658 lines changed: 90, context: html, text, full: html, text
    Added missing bedGraph data range settings (minLimit and maxLimit) based on commented-out type bigWig lines that specify range.
  • 1.657 lines changed: 40, context: html, text, full: html, text
    fix long label and some view setting for CSHL short RNA-seq
  • 1.656 lines changed: 28, context: html, text, full: html, text
    Removing PI name from lab in Caltech track
  • 1.655 lines changed: 28, context: html, text, full: html, text
    Correcting ENCODE grant/lab metadata for Caltech RNA
  • 1.654 lines changed: 6, context: html, text, full: html, text
    fix up prostate signals
  • 1.653 lines changed: 51, context: html, text, full: html, text
    fix short labels for GIS RNA Pet
  • 1.652 lines changed: 664, context: html, text, full: html, text
    add GIS RNA PET back in
  • 1.651 lines changed: 422, context: html, text, full: html, text
    take out GIS Pet Rna
  • 1.650 lines changed: 33, context: html, text, full: html, text
    fix up the long labels for GIS RNA-seq
  • 1.649 lines changed: 54, context: html, text, full: html, text
    change Cshl short RNA-seq to use bedGraph instead of bigWig
  • 1.648 lines changed: 36, context: html, text, full: html, text
    change GIS signal tracks to normal wiggles and make them LOG
  • 1.647 lines changed: 15, context: html, text, full: html, text
    make LOG the default transform for CSHL long RNA-seq signals
  • 1.646 lines changed: 30, context: html, text, full: html, text
    changing CSHL long RNA-seq signal tracks to bedGraph
  • 1.645 lines changed: 18, context: html, text, full: html, text
    Finish (I hope) Base Overlap updates from Open Chromatin release 2
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed minor typos.
  • 1.6 lines changed: 35, context: html, text, full: html, text
    Fixing file to conform to 80char line limit.
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
  • 1.1 lines changed: 55, context: html, text, full: html, text
    Description for Burge lab RNA-seq data mapped with GEM mapper.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.60 lines changed: 1, context: html, text, full: html, text
    set primate chain/Net to hide
  • 1.59 lines changed: 10, context: html, text, full: html, text
    added track block for Alt Events
  • 1.58 lines changed: 107, context: html, text, full: html, text
    added Burge lab data mapped using GEM mapper.
  • 1.57 lines changed: 6, context: html, text, full: html, text
    The 46-way phastCons and phyloP tracks turn back to the old style wiggle tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.470 lines changed: 24, context: html, text, full: html, text
    Add liftover chain tracks for newer assemblies
• src/hg/near/hgNear/hgNearData/cdsScore.html
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Rewrote action setion to drop broken link, redirect another link to a better location, and make the section more clear.
• src/hg/near/hgNear/hgNearData/entrezGene.html
  • 1.3 lines changed: 6, context: html, text, full: html, text
    fixed outdated information about OMIM links on Entrez records
• src/hg/oneShot/freen/freen.c
  • 1.92 lines changed: 7, context: html, text, full: html, text
    More zlib testing.
  • 1.91 lines changed: 10, context: html, text, full: html, text
    Testing zlibFace.
• src/hg/tcga/bamBam/bamBamCNV.c
  • 1.3 lines changed: 26, context: html, text, full: html, text
    generalized bam_dual to avoid kent libraries
• src/hg/tcga/bamBam/bam_dual_pileup.c
  • 1.9 lines changed: 43, context: html, text, full: html, text
    added comments
  • 1.8 lines changed: 27, context: html, text, full: html, text
    generalized bam_dual to avoid kent libraries
• src/hg/tcga/bamBam/example_dual.c
  • 1.1 lines changed: 155, context: html, text, full: html, text
    initial commit
• src/hg/txCds/txCdsRedoUniprotPicks/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work.
• src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
  • 1.1 lines changed: 148, context: html, text, full: html, text
    Seems to work.
• src/inc/bbiFile.h
  • 1.19 lines changed: 21, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.18 lines changed: 7, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/inc/bigWig.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/inc/common.h
  • 1.158 lines changed: 15, context: html, text, full: html, text
    Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders.
• src/inc/dystring.h
  • 1.20 lines changed: 4, context: html, text, full: html, text
    Adding dyStringWriteOne.
• src/inc/hash.h
  • 1.50 lines changed: 4, context: html, text, full: html, text
    Added hashFindValUpperCase (based on hashLookupUpperCase).
• src/inc/net.h
  • 1.36 lines changed: 7, context: html, text, full: html, text
    Added netUrlOpenSockets/netGetOpenFtpSockets, which can pass the FTP control socket back to the caller instead of forking for the sake of closing the control socket immediately. This prevents the accumulation of zombie (defunct) child processes forked from the udcFuse daemon, and saves a bit of overhead. netUrl byterange can now be open-ended (only the start offset is specified), which also supports persistent connections in udcFuse. Also did some refactoring (readability & error messages).
  • 1.35 lines changed: 2, context: html, text, full: html, text
    Force keys to uppercase for netUrlHead's hash, for case-insensitive lookup. Also, in udcInfoViaHttp, accept Date: as a poor substitute for missing Last-Modified:.
• src/inc/udc.h
  • 1.16 lines changed: 24, context: html, text, full: html, text
    Use net.c's new support for open-ended byterange and sockets that stay open, so that we can read successive data blocks from the same socket, instead of reconnecting to the remote server for each successive chunk. This dramatically improves the performance of udcFuse on block-compressed data. Refactored to reduce code duplication between ftp and http fetchData methods, and keep private struct & methods out of udc.h. Added checking of return value from fetchData; we were just writing a bunch of 0's to sparseData when fetchData returned fewer bytes than we asked for [error while debugging net.c], which resulted in corrupt sparseData file.
• src/inc/zlibFace.h
  • 1.1 lines changed: 26, context: html, text, full: html, text
    Adding zlib interface routines.
• src/lib/bbiRead.c
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Making assumptions of bbiTotalSummary vs. version numbers a bit more explicit in response to Angie's feedback.
  • 1.15 lines changed: 59, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bbiWrite.c
  • 1.10 lines changed: 75, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.9 lines changed: 74, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bigBed.c
  • 1.23 lines changed: 46, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/lib/bwgCreate.c
  • 1.21 lines changed: 19, context: html, text, full: html, text
    Improving calculations about initial zoom level in wigToBigWig, especially for compressed files.
  • 1.20 lines changed: 125, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/bwgQuery.c
  • 1.23 lines changed: 111, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/lib/cirTree.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Removing some commented out debugging statements.
• src/lib/common.c
  • 1.136 lines changed: 33, context: html, text, full: html, text
    Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders.
• src/lib/dystring.c
  • 1.25 lines changed: 4, context: html, text, full: html, text
    Adding dyStringWriteOne.
• src/lib/gifLabel.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Changing uglyf to printf since it's not just a temporary thing.
• src/lib/hash.c
  • 1.51 lines changed: 10, context: html, text, full: html, text
    Added hashFindValUpperCase (based on hashLookupUpperCase).
• src/lib/makefile
  • 1.155 lines changed: 1, context: html, text, full: html, text
    Adding zlib interface routines.
• src/lib/net.c
  • 1.77 lines changed: 310, context: html, text, full: html, text
    Added netUrlOpenSockets/netGetOpenFtpSockets, which can pass the FTP control socket back to the caller instead of forking for the sake of closing the control socket immediately. This prevents the accumulation of zombie (defunct) child processes forked from the udcFuse daemon, and saves a bit of overhead. netUrl byterange can now be open-ended (only the start offset is specified), which also supports persistent connections in udcFuse. Also did some refactoring (readability & error messages).
  • 1.76 lines changed: 3, context: html, text, full: html, text
    Force keys to uppercase for netUrlHead's hash, for case-insensitive lookup. Also, in udcInfoViaHttp, accept Date: as a poor substitute for missing Last-Modified:.
• src/lib/udc.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Oops, last-minute bug that negated performace gain :).
  • 1.26 lines changed: 166, context: html, text, full: html, text
    Use net.c's new support for open-ended byterange and sockets that stay open, so that we can read successive data blocks from the same socket, instead of reconnecting to the remote server for each successive chunk. This dramatically improves the performance of udcFuse on block-compressed data. Refactored to reduce code duplication between ftp and http fetchData methods, and keep private struct & methods out of udc.h. Added checking of return value from fetchData; we were just writing a bunch of 0's to sparseData when fetchData returned fewer bytes than we asked for [error while debugging net.c], which resulted in corrupt sparseData file.
  • 1.25 lines changed: 9, context: html, text, full: html, text
    Force keys to uppercase for netUrlHead's hash, for case-insensitive lookup. Also, in udcInfoViaHttp, accept Date: as a poor substitute for missing Last-Modified:.
• src/lib/zlibFace.c
  • 1.1 lines changed: 91, context: html, text, full: html, text
    Adding zlib interface routines.
• src/product/README.install
  • 1.12 lines changed: 11, context: html, text, full: html, text
    Fixed up comment about fixed WEBROOT location
• src/utils/ave/ave.c
  • 1.9 lines changed: 61, context: html, text, full: html, text
    Add -noQuartiles option
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.21 lines changed: 2, context: html, text, full: html, text
    Fixed bug in sumSquares.
  • 1.20 lines changed: 69, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.19 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedGraphToBigWig/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.19 lines changed: 2, context: html, text, full: html, text
    Fixed bug in sumSquares.
  • 1.18 lines changed: 61, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.17 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bedToBigBed/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigBedInfo/bigBedInfo.c
  • 1.2 lines changed: 26, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/bigBedInfo/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/bigBedSummary/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigBedToBed/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.6 lines changed: 21, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
  • 1.5 lines changed: 2, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigInfo/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigSummary/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigToBedGraph/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/bigWigToWig/bigWigToWig.c
  • 1.1 lines changed: 79, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/bigWigToWig/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/faCmp/faCmp.c
  • 1.8 lines changed: 14, context: html, text, full: html, text
    use different exit code when differences are detected to make it easy to use in scripts
• src/utils/htmlCheck/htmlCheck.c
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Force keys to uppercase for netUrlHead's hash, for case-insensitive lookup. Also, in udcInfoViaHttp, accept Date: as a poor substitute for missing Last-Modified:.
• src/utils/makefile
  • 1.74 lines changed: 1, context: html, text, full: html, text
    Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph.
• src/utils/qa/getDbSize.csh
  • 1.15 lines changed: 7, context: html, text, full: html, text
    mentioned files in usage statement. removed redundant statement about defaults to beta. removed code that restricts to dev as it runs ok on beta, too. per brooke
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.89 lines changed: 2, context: html, text, full: html, text
    v220 preview
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • 1.20 lines changed: 8, context: html, text, full: html, text
    using flag to produce separate insert statements in dump
  • 1.19 lines changed: 4, context: html, text, full: html, text
    TODO note
• src/utils/raToLines/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removing unused library.
• src/utils/scaffoldFaToAgp/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little.
• src/utils/wigToBigWig/expected/tf1.sum
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Updating expected output.
• src/utils/wigToBigWig/expected/tf3.sum
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updating expected output.
• src/utils/wigToBigWig/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Making compression the default for the bigBed and bigWig creators.
  • 1.8 lines changed: 10, context: html, text, full: html, text
    First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed.

• lines changed: 7998
• files changed: 111