CVS changes by file

review to branch (2009-11-03 to 2009-11-10) v219

• src/fuse/udcFuse/makefile
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Don't add -lfuse here, leave that to common.mk if USE_FUSE==1.
• src/fuse/udcFuse/udcFuse.c
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Doh, forgot to leave in a dummy main when USE_FUSE is not defined (thanks Tim!).
  • 1.3 lines changed: 7, context: html, text, full: html, text
    Added #ifdef USE_FUSE wrapper so this won't break compiles on machines that don't have fuse installed (thanks Mark!). Also, use appropriately sized int for cache file size, and merge adjacent errCatch wrappers.
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Set the udc cache timeout to an hour [need to add refresh button to hgTrackUi, then can make timeout very large], and if cache files are younger than that, use kernel caching (on top of udc's faster open) for almost-local performance.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.141 lines changed: 21, context: html, text, full: html, text
    Added MCF-7 protocol for Farnham and removed the obsolete HA antibody listing
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.3 lines changed: 47, context: html, text, full: html, text
    Reorder so lab (which is key) is first
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adjust lab name to match projects table
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.2 lines changed: 45, context: html, text, full: html, text
    Fix lab to project mapping
• src/hg/hgCustom/hgCustom.c
  • 1.134 lines changed: 1, context: html, text, full: html, text
    Call customFactoryEnableExtraChecking -- initial load is a good time to perform more expensive tests.
• src/hg/hgGene/hgGeneData/Human/links.ra
  • 1.37 lines changed: 7, context: html, text, full: html, text
    Added GeneNetwork link.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.507 lines changed: 4, context: html, text, full: html, text
    Fixup chainNet composite Ui
• src/hg/hgTracks/bedTrack.c
  • 1.19 lines changed: 7, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/bigWigTrack.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/expRatioTracks.c
  • 1.45 lines changed: 1, context: html, text, full: html, text
    set correct clipping rectangle
• src/hg/hgTracks/hgTracks.c
  • 1.1604 lines changed: 28, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/hgTracks.h
  • 1.189 lines changed: 11, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/mafTrack.h
  • 1.9 lines changed: 1, context: html, text, full: html, text
    put summary view back to 1000000
• src/hg/hgTracks/simpleTracks.c
  • 1.110 lines changed: 9, context: html, text, full: html, text
    Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete.
• src/hg/hgTracks/wigCommon.h
  • 1.8 lines changed: 3, context: html, text, full: html, text
    add transform function for wiggles
• src/hg/hgTracks/wigTrack.c
  • 1.94 lines changed: 7, context: html, text, full: html, text
    add transform function for wiggles
• src/hg/hgc/lowelab.c
  • 1.40 lines changed: 113, context: html, text, full: html, text
    Adding vecscreen and orthologs
• src/hg/inc/customFactory.h
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Added customFactoryEnableExtraChecking, intended to be called only by hgCustom. When the user first loads a custom track, it's a good time for more expensive testing (like opening remote BAM files). However, hgTracks etc. can save time by not duplicating that work every time they parse existing tracks. Currently only bamLoader uses this.
• src/hg/inc/customTrack.h
  • 1.56 lines changed: 1, context: html, text, full: html, text
    Adding bbiFile field to customTrack to avoid reopening it repeatedly.
• src/hg/inc/hui.h
  • 1.141 lines changed: 9, context: html, text, full: html, text
    add transform function for wiggles
• src/hg/inc/megablastInfo.h
  • 1.1 lines changed: 70, context: html, text, full: html, text
    Adding megablast track
• src/hg/inc/versionInfo.h
  • 1.160 lines changed: 1, context: html, text, full: html, text
    "New version number v219"
  • 1.159 lines changed: 1, context: html, text, full: html, text
    "New version number v217"
• src/hg/inc/wiggle.h
  • 1.87 lines changed: 7, context: html, text, full: html, text
    add transform function for wiggles
• src/hg/instinct/hgPathways/hgCircleMaps.c
  • 1.16 lines changed: 9, context: html, text, full: html, text
    Bunch of updates to make this work, and slightly change the UI
• src/hg/instinct/hgPathways/hgPathways.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Bunch of updates to make this work, and slightly change the UI
• src/hg/instinct/hgPathways/hgPathways.h
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Bunch of updates to make this work, and slightly change the UI
• src/hg/instinct/hgPathways/hgPathwaysFrontend/index.html
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Bunch of updates to make this work, and slightly change the UI
• src/hg/instinct/hgPathways/hgPathwaysFrontend/js/hgHeatPath.js
  • 1.14 lines changed: 18, context: html, text, full: html, text
    Bunch of updates to make this work, and slightly change the UI
• src/hg/lib/bamFile.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    Don't use kentlib free functions on mem returned from samtools, because kentlib functions weren't used to allocate it.
  • 1.13 lines changed: 49, context: html, text, full: html, text
    It's not sufficient to test existence of a path in udcFuse, because empty directories are left behind when bitmap and sparseData files are cleaned up, and then udcFuse will show the directory. So test whether a udcFuse path is a regular file (as a dir with bitmap and sparseData files will appear). Also, test existence of index files independently from .bam, and look for both index possibilities as udcFuse paths before attempting the costly udc open.
• src/hg/lib/customFactory.c
  • 1.110 lines changed: 23, context: html, text, full: html, text
    Adding bbiFile field to customTrack to avoid reopening it repeatedly. Setting display limits from bigWig/bigBed files so they don't end up the weird 0-127 defaults.
  • 1.109 lines changed: 15, context: html, text, full: html, text
    Added customFactoryEnableExtraChecking, intended to be called only by hgCustom. When the user first loads a custom track, it's a good time for more expensive testing (like opening remote BAM files). However, hgTracks etc. can save time by not duplicating that work every time they parse existing tracks. Currently only bamLoader uses this.
  • 1.108 lines changed: 2, context: html, text, full: html, text
    Handle chromosomes setting in customTrackUpdateFromSettings, to avoid hgTracks loading overhead for a custom track that has no data on the current chrom.
• src/hg/lib/hui.c
  • 1.246 lines changed: 28, context: html, text, full: html, text
    add transform function for wiggles
  • 1.245 lines changed: 18, context: html, text, full: html, text
    Added support in controlled vocabulary link to support suffix that is not pare of the link
• src/hg/lib/makefile
  • 1.399 lines changed: 1, context: html, text, full: html, text
    Adding megablast
• src/hg/lib/megablastInfo.as
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Adding megablast track
• src/hg/lib/megablastInfo.c
  • 1.1 lines changed: 169, context: html, text, full: html, text
    Adding megablast track
• src/hg/lib/megablastInfo.sql
  • 1.1 lines changed: 20, context: html, text, full: html, text
    Adding megablast track
• src/hg/lib/wiggleCart.c
  • 1.24 lines changed: 111, context: html, text, full: html, text
    Hopefully making wiggle limits behave a little nicer when defaults are not set. Certainly works nicer with bigWig
  • 1.23 lines changed: 25, context: html, text, full: html, text
    add transform function for wiggles
• src/hg/makeDb/doc/encodeDccHg18/GisDnaPet.txt
  • 1.1 lines changed: 13, context: html, text, full: html, text
    initial/current status
• src/hg/makeDb/doc/encodeDccHg18/GisRnaPet.txt
  • 1.1 lines changed: 14, context: html, text, full: html, text
    initial/current status
• src/hg/makeDb/doc/encodeDccHg18/GisRnaSeq.txt
  • 1.1 lines changed: 5, context: html, text, full: html, text
    initial/current status
• src/hg/makeDb/doc/hg17.txt
  • 1.125 lines changed: 5, context: html, text, full: html, text
    added comment about changing colors in dgv
  • 1.124 lines changed: 1, context: html, text, full: html, text
    added comment about changing colors in dgv
• src/hg/makeDb/doc/hg18.txt
  • 1.388 lines changed: 14, context: html, text, full: html, text
    Added GeneNetwork ID table for hgGene link to GeneNetwork.
  • 1.387 lines changed: 5, context: html, text, full: html, text
    added comment about changing colors in dgv
  • 1.386 lines changed: 1, context: html, text, full: html, text
    added comment about changing colors in dgv
• src/hg/makeDb/doc/hg19.txt
  • 1.60 lines changed: 14, context: html, text, full: html, text
    Documented the chrom names that were corrected and made a note that the otherSize column could be dropped in future for the seg dupes data.
  • 1.59 lines changed: 1, context: html, text, full: html, text
    Added extra line in seg dupes track documentation.
  • 1.58 lines changed: 2, context: html, text, full: html, text
    File cleanup for seg dupes.
  • 1.57 lines changed: 42, context: html, text, full: html, text
    Re-loaded segmental duplications data after correcting chromosome names.
  • 1.56 lines changed: 27, context: html, text, full: html, text
    Added segmental duplications provided by Eichler lab.
  • 1.55 lines changed: 16, context: html, text, full: html, text
    finish up hgPal download
• src/hg/makeDb/doc/mm9.txt
  • 1.116 lines changed: 15, context: html, text, full: html, text
    Added GeneNetowork ID table for hgGene link to GeneNetwork.
• src/hg/makeDb/doc/rn4.txt
  • 1.35 lines changed: 14, context: html, text, full: html, text
    Added GeneNetwork ID table to enable hgGene link to GeneNetwork.
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.97 lines changed: 14, context: html, text, full: html, text
    added ignore entries
  • 1.96 lines changed: 1, context: html, text, full: html, text
    added ignore entry
• src/hg/makeDb/schema/all.joiner
  • 1.742 lines changed: 2, context: html, text, full: html, text
    Added a wild card to the ends of phastCons tables (in tablesIgnored).
• src/hg/makeDb/trackDb/genomicSuperDups.html
  • 1.14 lines changed: 14, context: html, text, full: html, text
    Added text to methods and another reference as requested by Eicher lab. Added data provider for the hg19 data for this track.
• src/hg/makeDb/trackDb/gnfAtlas2.html
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Updated description of display of all tissues vs. display of averages.
• src/hg/makeDb/trackDb/horse/equCab2/trackDb.ra
  • 1.9 lines changed: 4, context: html, text, full: html, text
    putting the species in Conservation track in proper phylo-order
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.11 lines changed: 4, context: html, text, full: html, text
    more stuff for monDom5 CN override
  • 1.10 lines changed: 3, context: html, text, full: html, text
    override for monDom5 ChainNet track
  • 1.9 lines changed: 6, context: html, text, full: html, text
    putting chicken chain/net in the correct order
  • 1.8 lines changed: 8, context: html, text, full: html, text
    collapsing chainMm9 and chainMm9 override blocks into one block
  • 1.7 lines changed: 4, context: html, text, full: html, text
    putting the chain and net tracks in phylo order
• src/hg/makeDb/trackDb/human/gnfAtlas2.html
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Updated description of display of all tissues vs. display of averages.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.644 lines changed: 196, context: html, text, full: html, text
    Added subgroup5 for HudsonAlpha... planning for 5 dimensions to come
  • 1.643 lines changed: 13, context: html, text, full: html, text
    add bounds to bigWig
  • 1.642 lines changed: 139, context: html, text, full: html, text
    GIS RNA-seq signal tracks
  • 1.641 lines changed: 2, context: html, text, full: html, text
    Fix another line format error in UW ChIP seq entry
  • 1.640 lines changed: 2, context: html, text, full: html, text
    Fix line format error in UW ChIP seq entry
  • 1.639 lines changed: 35, context: html, text, full: html, text
    35 of 41 Base Overlap tracks for ChromatinMap were replaced.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
  • 1.5 lines changed: 28, context: html, text, full: html, text
    Edits for clarity
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixup some dates on assemblies
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Add reference to new paper on phyloP
  • 1.1 lines changed: 578, context: html, text, full: html, text
    Copied from the hg18 44way and updated for 46 way specifics
• src/hg/makeDb/trackDb/human/omimGene.html
  • 1.22 lines changed: 1, context: html, text, full: html, text
    typo. thnx, ann.
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.88 lines changed: 9, context: html, text, full: html, text
    Adding vecscreen track
• src/hg/makeDb/trackDb/makefile
  • 1.277 lines changed: 1, context: html, text, full: html, text
    Adding susScr1 to the build
• src/hg/makeDb/trackDb/mouse/gnfAtlas2.html
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Updated description of display of all tissues vs. display of averages.
• src/hg/makeDb/trackDb/pig/susScr1/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr1/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr1/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/pig/susScr1/trackDb.ra
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/gnfAtlas2.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Updated description of display of all tissues vs. display of averages.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.537 lines changed: 33, context: html, text, full: html, text
    collapsing exactly idential release alpha/beta blocks into one (for chain and net of galGal3)
• src/hg/makeDb/trackDb/worm/ce4/description.html
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to v170 versions.
• src/hg/makeDb/trackDb/worm/ce4/gap.html
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to v170 versions.
• src/hg/makeDb/trackDb/worm/ce4/gold.html
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to v170 versions.
• src/hg/makeDb/trackDb/worm/ce5/description.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/makeDb/trackDb/worm/ce5/gap.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/makeDb/trackDb/worm/ce5/gold.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/makeDb/trackDb/worm/ce6/description.html
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/makeDb/trackDb/worm/ce6/gap.html
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/makeDb/trackDb/worm/ce6/gold.html
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Restored wormbase links to assembly-specific versions.
• src/hg/oneShot/freen/freen.c
  • 1.90 lines changed: 23, context: html, text, full: html, text
    Testing zlib compress and uncompress.
• src/hg/oneShot/freen/makefile
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Testing zlib compress and uncompress.
• src/hg/tcga/bamBam/bamBam.c
  • 1.9 lines changed: 130, context: html, text, full: html, text
    updated
• src/hg/tcga/bamBam/bamBamCNV.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    added file
  • 1.1 lines changed: 271, context: html, text, full: html, text
    added file
• src/hg/tcga/bamBam/bam_dual_pileup.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    updated
• src/hg/tcga/bamBam/makefile
  • 1.3 lines changed: 17, context: html, text, full: html, text
    added file
  • 1.2 lines changed: 4, context: html, text, full: html, text
    updated
• src/hg/utils/automation/Encode.pm
  • 1.50 lines changed: 10, context: html, text, full: html, text
    Fix key for 'pi' file -- should be 'lab'
• src/inc/bbiFile.h
  • 1.17 lines changed: 3, context: html, text, full: html, text
    adding bbiSummaryElementWrite
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Adding bbiTotalSummary.
  • 1.15 lines changed: 25, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/inc/bigBed.h
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Adding bigBedAutoSqlText.
• src/inc/bigWig.h
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/inc/common.mk
  • 1.74 lines changed: 9, context: html, text, full: html, text
    Added off-by-default USE_FUSE so udcFuse won't break compiles on machines that don't have fuse installed (thanks Mark!).
• src/inc/udc.h
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Oops, forgot that file size really needs to be a long long.
  • 1.14 lines changed: 12, context: html, text, full: html, text
    More changes motivated by udcFuse performance: added udcCacheAge, udcCacheTimeout and udcSetCacheTimeout. If cache files exist and are younger than the cache timeout threshold, don't fetch info from the remote server when opening, just use size and date from bitmap file. This saves 0.8s per open for ftp to NCBI. By default, cache timeout is 0 (same behavior as before -- always fetch info).
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Adding udcReadDouble.
  • 1.12 lines changed: 3, context: html, text, full: html, text
    Adding udcReadFloat function.
• src/lib/bbiRead.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    Updating bbiOpen to handle totalSummary.
  • 1.13 lines changed: 70, context: html, text, full: html, text
    Adding bbiTotalSummary.
• src/lib/bbiWrite.c
  • 1.8 lines changed: 10, context: html, text, full: html, text
    adding bbiSummaryElementWrite
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/lib/bigBed.c
  • 1.22 lines changed: 12, context: html, text, full: html, text
    Adding bigBedAutoSqlText.
• src/lib/bwgCreate.c
  • 1.19 lines changed: 40, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/lib/bwgQuery.c
  • 1.22 lines changed: 9, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/lib/udc.c
  • 1.24 lines changed: 4, context: html, text, full: html, text
    Oops, forgot that file size really needs to be a long long.
  • 1.23 lines changed: 68, context: html, text, full: html, text
    More changes motivated by udcFuse performance: added udcCacheAge, udcCacheTimeout and udcSetCacheTimeout. If cache files exist and are younger than the cache timeout threshold, don't fetch info from the remote server when opening, just use size and date from bitmap file. This saves 0.8s per open for ftp to NCBI. By default, cache timeout is 0 (same behavior as before -- always fetch info).
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Yikes! Stray 'else' could have led to mem corruption (use after free).
  • 1.21 lines changed: 10, context: html, text, full: html, text
    Adding udcReadDouble.
  • 1.20 lines changed: 10, context: html, text, full: html, text
    Adding udcReadFloat function.
• src/makefile
  • 1.70 lines changed: 1, context: html, text, full: html, text
    adding bigBedInfo util
• src/product/README.building.source
  • 1.18 lines changed: 15, context: html, text, full: html, text
    documenting SSL option
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • 1.18 lines changed: 42, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Adding version number to usage statement.
  • 1.16 lines changed: 12, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent. Also fixing bug with sumSquares being just sum.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Changing default blockSize and itemsPerSlot to something more reasonable.
  • 1.15 lines changed: 47, context: html, text, full: html, text
    Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default.
  • 1.14 lines changed: 4, context: html, text, full: html, text
    Adding version number to usage statement.
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Fixing bug where sumSquares was actually just sum.
  • 1.12 lines changed: 7, context: html, text, full: html, text
    Bumping version number. Making sectionCount and zoomCount more consistent.
• src/utils/bigBedInfo/bigBedInfo.c
  • 1.1 lines changed: 78, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigBedInfo/makefile
  • 1.2 lines changed: 10, context: html, text, full: html, text
    fixing makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigBedInfo/test.bed
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Utility to get information on a bigBed seems to work.
• src/utils/bigBedSummary/makefile
  • 1.8 lines changed: 2, context: html, text, full: html, text
    fixing makefile
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Adding additional information to bigWigInfo output - data and index sizes.
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Making listing of chromosomes just an option. Adding info from totalSummary, which some day may be used to set min/max values of bigBed/bigWig wiggle ranges.
• src/utils/bigWigSummary/bigWigSummary.c
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Making bigWigSummary functions take a bbiFile rather than a fileName.
• src/utils/mkUsageIndex.sh
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Updated for todays source tree particularies
• src/utils/qa/checkPushedFiles.csh
  • 1.2 lines changed: 35, context: html, text, full: html, text
    Changed this to accept a website and list of files rather than a list of files that includes most of the path and no machine. Also added filename: to output.
• src/utils/qa/getDbSize.csh
  • 1.14 lines changed: 47, context: html, text, full: html, text
    added support for gbdb files and disabled noIndex option. fixed to accomodate MySQL 5 TABLE STATUS dumps
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.88 lines changed: 3, context: html, text, full: html, text
    v219 final build
• src/utils/qa/weeklybld/doNewBranch.csh
  • 1.33 lines changed: 46, context: html, text, full: html, text
    rearranging the order of background operations so that utils do not hold up cgi and cvs-reports
• src/utils/qa/weeklybld/moveBranchTag.csh
  • 1.24 lines changed: 2, context: html, text, full: html, text
    fix beta tag so that it does not move until the cgis are pushed and released to the RR
• src/utils/qa/weeklybld/tagBeta.csh
  • 1.1 lines changed: 50, context: html, text, full: html, text
    fix beta tag so that it does not move until the cgis are pushed and released to the RR
• src/utils/qa/weeklybld/tagNewBranch.csh
  • 1.12 lines changed: 11, context: html, text, full: html, text
    fix beta tag so that it does not move until the cgis are pushed and released to the RR
• src/utils/wigToBigWig/wigToBigWig.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Adding version number to usage statement.

• lines changed: 3759
• files changed: 111