CVS changes by file

review to branch (2009-11-17 to 2009-12-01) v220

• src/cdnaAli/cdnaOff/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/cdnaAli/findCdna/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/fuse/udcFuse/udcFuse.c
  • 1.6 lines changed: 39, context: html, text, full: html, text
    Path may now include http auth info (that's the only way of communicating the info to udcFuse) -- if so, strip it out when making the udc cache path.
  • 1.5 lines changed: 10, context: html, text, full: html, text
    Debug message improvements.
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.22 lines changed: 119, context: html, text, full: html, text
    add code to parse genbank file for lowelab data source
• src/hg/encode/DAFs/DukeExons.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    duke affy exons
• src/hg/encode/DAFs/UwExons.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Uw Exon arrays
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.145 lines changed: 55, context: html, text, full: html, text
    Added 5 more antibodies for Myers
  • 1.144 lines changed: 33, context: html, text, full: html, text
    Added BCL11A, BCL3 and BHLHE40 for Myers
  • 1.143 lines changed: 1, context: html, text, full: html, text
    Add color (green) to H1 es cells
  • 1.142 lines changed: 213, context: html, text, full: html, text
    Add tags field (unique, no special chars, alpha start) to each entry
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.22 lines changed: 5, context: html, text, full: html, text
    make validationSettings required; fix some typos ("type in" => "type int")
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Need to force all labs in Snyder project to be the same, for now
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Save changed experiment
  • 1.3 lines changed: 132, context: html, text, full: html, text
    Improved status handling
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.203 lines changed: 10, context: html, text, full: html, text
    make -database required if they are using -validateFile; remove "NULL"
  • 1.202 lines changed: 42, context: html, text, full: html, text
    1. Remove hg18 hardcoding 2. Use newly added 'tag' field from CV instead of 'term'
  • 1.201 lines changed: 5, context: html, text, full: html, text
    add -database option
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • 1.6 lines changed: 3, context: html, text, full: html, text
    update expected files to accomodate doEncodeValidate.pl changes
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    update expected files to accomodate doEncodeValidate.pl changes
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.hg18.1.txt.BED
  • 1.3 lines changed: 5000, context: html, text, full: html, text
    fix bed coordinates and delete lines that have more than 3 mismatches
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.hg18.2.txt.BED
  • 1.3 lines changed: 5000, context: html, text, full: html, text
    fix bed coordinates and delete lines that have more than 3 mismatches
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • 1.9 lines changed: 1, context: html, text, full: html, text
    add validationSettings
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.52 lines changed: 7, context: html, text, full: html, text
    Removed anyWild(), it was added to common.c.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.508 lines changed: 5, context: html, text, full: html, text
    Change bam cart variable names and bamTrack code to use Tim's cart and trackDb ClosestToHome API.
• src/hg/hgTracks/bamTrack.c
  • 1.18 lines changed: 46, context: html, text, full: html, text
    Change bam cart variable names and bamTrack code to use Tim's cart and trackDb ClosestToHome API.
  • 1.17 lines changed: 21, context: html, text, full: html, text
    Add pairSearchRange setting-controlled extra search for improperly paired items' mates that didn't happen to fall in the viewing window, a la hgc/bamClick.c.
  • 1.16 lines changed: 6, context: html, text, full: html, text
    Needed to be a bit more careful setting both stub coordinates and lfs->end -- was getting lfs->end too short, resulting in too short cachedDna in cds.c in some cases.
• src/hg/hgTracks/bedTrack.c
  • 1.20 lines changed: 52, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/bigBedTrack.c
  • 1.1 lines changed: 123, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/bigWigTrack.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/hgTracks.c
  • 1.1609 lines changed: 8, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
  • 1.1608 lines changed: 7, context: html, text, full: html, text
    Fix bug Rachel found with imageV2 framework, where BLAT sequence track was being forced to the bottom.
• src/hg/hgTracks/hgTracks.h
  • 1.193 lines changed: 27, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/makefile
  • 1.89 lines changed: 2, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/simpleTracks.c
  • 1.114 lines changed: 21, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/wigTrack.c
  • 1.98 lines changed: 2, context: html, text, full: html, text
    Removing whiskers when got more pixels than bases in window.
  • 1.97 lines changed: 3, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
• src/hg/hgc/bamClick.c
  • 1.12 lines changed: 18, context: html, text, full: html, text
    Refinements to searching for mates out of window: don't do the extra bamFetch unless pairSearchRange > 0; increase default pairSearchRange default; clip start of window at 0; there's only one item name, so don't need to loop on pairHash name.
• src/hg/inc/hui.h
  • 1.143 lines changed: 1, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
• src/hg/inc/versionInfo.h
  • 1.161 lines changed: 1, context: html, text, full: html, text
    "New version number v220"
• src/hg/inc/wiggle.h
  • 1.89 lines changed: 1, context: html, text, full: html, text
    premature, need to wait for trackDb to update before eliminating the recognition of defaultViewLimits
  • 1.88 lines changed: 1, context: html, text, full: html, text
    eliminate defaultViewLimits it is all viewLimits now
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.81 lines changed: 4, context: html, text, full: html, text
    Changed getDatasets() to return datasets in priority order within a group
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_gray2009_OVcellLines.ra
  • 1.1 lines changed: 216, context: html, text, full: html, text
    Ovarian cell line data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.4 lines changed: 267, context: html, text, full: html, text
    new clinical data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAopen.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    fixed the patDbs on the integrated sets
  • 1.9 lines changed: 3, context: html, text, full: html, text
    fixed the patDbs on the integrated sets
  • 1.8 lines changed: 59, context: html, text, full: html, text
    Added integrated datasets for all batches
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.gray2009.ra
  • 1.1 lines changed: 39, context: html, text, full: html, text
    Ovarian cell line data
• src/hg/instinct/makefile
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Removed making subjectView
• src/hg/instinct/subjectView/subjectView.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    fixed genoheatmap ref to url member
• src/hg/js/hgTracks.js
  • 1.47 lines changed: 18, context: html, text, full: html, text
    some browser specific changes for right-click code (currently dead code)
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Fix for bug Angie found which sets position to 1bp on hgc click
• src/hg/js/jquery.tablednd.js
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Added dragStartIndex to be returned by onDrag() callback.
• src/hg/js/utils.js
  • 1.26 lines changed: 11, context: html, text, full: html, text
    Added support for calling warnBox insteadf of alert. Now a list of messages can be created, just as from C.
• src/hg/lib/bamFile.c
  • 1.16 lines changed: 28, context: html, text, full: html, text
    Since samtools' bam_index_load saves .bai files to the current directory, change to a trashDir when calling it (instead of using a locally hacked samtools).
  • 1.15 lines changed: 5, context: html, text, full: html, text
    Include http auth string in udcFuse path because udcFuse has no other way to get the auth.
• src/hg/lib/cart.c
  • 1.113 lines changed: 1, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).
• src/hg/lib/customFactory.c
  • 1.111 lines changed: 22, context: html, text, full: html, text
    removed temporary variable no longer needed in transtion from name dataUrl to bigDataUrl
• src/hg/lib/hui.c
  • 1.250 lines changed: 2, context: html, text, full: html, text
    Jim requested no enforcement of view range limits
• src/hg/lib/trackDbCustom.c
  • 1.72 lines changed: 3, context: html, text, full: html, text
    Expanding size of buffer that looks like it is too small and may overflow someday.
• src/hg/lib/wiggleCart.c
  • 1.34 lines changed: 8, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Experimental change-a-comment commit because CVS is being quirky.
  • 1.32 lines changed: 10, context: html, text, full: html, text
    premature, need to wait for trackDb to update before eliminating the recognition of defaultViewLimits
  • 1.31 lines changed: 10, context: html, text, full: html, text
    eliminate defaultViewLimits it is all viewLimits now
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Display wigFetchMinMaxYWithCart's warning about missing data range settings only when we're on hgwdev.
  • 1.29 lines changed: 20, context: html, text, full: html, text
    Removed the clipping of viewing range to (optionally expanded) data range at Jim's request. Since that removes the purpose of expanding the data range to viewLimits or settingsByView's viewLimitsMax, I took that out too and those trackDb settings are now ignored & obsolete.
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Oops, logic bug prevented absMin from being set properly for wiggle (thanks again Jim!)
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Oops, used double instead of int for abs{Min,Max} -- thanks Jim!
• src/hg/makeDb/doc/bosTau4.txt
  • 1.19 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/bosTauMd3.txt
  • 1.4 lines changed: 14, context: html, text, full: html, text
    finishing touches on MD3 liftover
  • 1.3 lines changed: 21, context: html, text, full: html, text
    finish load and cleanup; add dbDb row
  • 1.2 lines changed: 12, context: html, text, full: html, text
    make liftover
  • 1.1 lines changed: 142, context: html, text, full: html, text
    adding MD3 so we can make chains to bosTau4
• src/hg/makeDb/doc/braFlo1.txt
  • 1.19 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/calJac1.txt
  • 1.21 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/cavPor3.txt
  • 1.21 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/ce1.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change defaultViewLimits to viewLimits
• src/hg/makeDb/doc/ce2.txt
  • 1.8 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/danRer2.txt
  • 1.6 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/danRer3.txt
  • 1.17 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/danRer4.txt
  • 1.35 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/dm1.txt
  • 1.5 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Added a couple of tagAlign files missing from the versioned files lists
• src/hg/makeDb/doc/encodeDccHg18/uwChIPseq.release1.notes.txt
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Minor fix of a referenece to Yale which should have been HudsonAlpha
  • 1.1 lines changed: 881, context: html, text, full: html, text
    Checkin for Thomas. Notes for UwChIPseq release1, because there are too many files to be listed in the pushQ.
• src/hg/makeDb/doc/ferrAcid1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/galGal1.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change defaultViewLimits to viewLimits
• src/hg/makeDb/doc/hg16.txt
  • 1.11 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/hg17.txt
  • 1.126 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/hg19.txt
  • 1.64 lines changed: 39, context: html, text, full: html, text
    Update genbank etc/genbank.conf to include upstreamMaf definitions, and phyloP track histograms
  • 1.63 lines changed: 16, context: html, text, full: html, text
    Proper calculation lodToBedScore for 46-way mostConserved tracks
  • 1.62 lines changed: 15, context: html, text, full: html, text
    Adding allenBrainGene.
• src/hg/makeDb/doc/metAce1.txt
  • 1.3 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/metMar1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methBark1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methBurt1.txt
  • 1.2 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methJann1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methKand1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methMaze1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/methTher1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/mm5.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/oryLat2.txt
  • 1.17 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/panTro1.txt
  • 1.8 lines changed: 2, context: html, text, full: html, text
    change autoScaleDefault to autoScale
  • 1.7 lines changed: 1, context: html, text, full: html, text
    change defaultViewLimits to viewLimits
• src/hg/makeDb/doc/petMar1.txt
  • 1.23 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/picrTorr1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/pyrAby1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/pyrAer1.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change defaultViewLimits to viewLimits
• src/hg/makeDb/doc/pyrFur2.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/pyrHor1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/rheMac2.txt
  • 1.19 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/sacCer1.txt
  • 1.10 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/sulSol1.txt
  • 1.2 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/sulfAcid1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/sulfToko1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/therAcid1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/therKoda1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/therVolc1.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.352 lines changed: 1, context: html, text, full: html, text
    turn on upstream maf for 46-way conservation on hg19
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.98 lines changed: 175, context: html, text, full: html, text
    added ignore entries
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.98 lines changed: 1, context: html, text, full: html, text
    updated tcga integrated sample ids
  • 1.97 lines changed: 28, context: html, text, full: html, text
    Added Ovarian Cell Line data
  • 1.96 lines changed: 25, context: html, text, full: html, text
    Added TCGA Ovarian Integrated datasets
• src/hg/makeDb/hgLoadWiggle/wigTableStats.sh
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Allow it to work on multiple tables in a single database
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Add viewLimits to usage message
  • 1.2 lines changed: 19, context: html, text, full: html, text
    Add viewLimits recommended calculation
  • 1.1 lines changed: 45, context: html, text, full: html, text
    Initial contents
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.55 lines changed: 139, context: html, text, full: html, text
    made subtrack processing check for more errors, fail on errors, and a lot easier to read without all the continues and huge functions. Confirmed that trackDb generated is the same as the old hgTrackDb (after fixing the 8 errors found in existing tracks). All of this is prep for automatically adding prefixes to subGroups for automatic sorting
  • 1.54 lines changed: 17, context: html, text, full: html, text
    Add -settings option for debug scanning of trackDb settings hash variables
• src/hg/makeDb/trackDb/README
  • 1.94 lines changed: 6, context: html, text, full: html, text
    Adding bigBed-specific optional field denseCoverage to trackDb system. One example of it is in wgEncodeGisRnaSeq.
  • 1.93 lines changed: 1, context: html, text, full: html, text
    Corrected typo.
  • 1.92 lines changed: 10, context: html, text, full: html, text
    Corrected typos.
  • 1.91 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra
  • 1.7 lines changed: 4, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/ancestor/canHg10/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/ancestor/canHg11/trackDb.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/ancestor/canHg4/trackDb.ra
  • 1.11 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to autoScale
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    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.17 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/zebrafish/danRer2/trackDb.ra
  • 1.34 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • 1.51 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.35 lines changed: 1, context: html, text, full: html, text
    change autoScaleDefault to autoScale
• src/hg/makeDb/trackDbPatch/makefile
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Creating patched files in -test mode now. Works for adding new fields, keeping comments and indentation level. Haven't tested yet for modifying existing fields.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Starting to work on utility to patch trackDb files. Just reads one of two inputs at the moment, no output.
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.2 lines changed: 298, context: html, text, full: html, text
    Creating patched files in -test mode now. Works for adding new fields, keeping comments and indentation level. Haven't tested yet for modifying existing fields.
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Starting to work on utility to patch trackDb files. Just reads one of two inputs at the moment, no output.
• src/hg/near/hgMapToGene/hgMapToGene.c
  • 1.16 lines changed: 11, context: html, text, full: html, text
    Adding ignoreStrand option.
• src/hg/near/hgNear/hgNear.c
  • 1.185 lines changed: 6, context: html, text, full: html, text
    Removing duplicate definition of anyWild (use the common.h/wildcmp.c version).
• src/hg/near/hgNear/hgNear.h
  • 1.99 lines changed: 3, context: html, text, full: html, text
    Removing duplicate definition of anyWild (use the common.h/wildcmp.c version).
• src/hg/near/hgNear/hgNearData/geneCategory.html
  • 1.8 lines changed: 3, context: html, text, full: html, text
    changed link so it goes to a page that better describes the gene categories
• src/hg/near/makeNear.doc
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
  • 1.1 lines changed: 114, context: html, text, full: html, text
    Utility to figure out missing bedGraph limits seems to work.
• src/hg/oneShot/findToFixBedGraphLimits/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Utility to figure out missing bedGraph limits seems to work.
• src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Bumping up recommended view range by another std on each side of mean.
  • 1.1 lines changed: 134, context: html, text, full: html, text
    One shot program to help patch viewLimits of bedGraph here.
• src/hg/oneShot/findToFixBedGraphViewLimits/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    One shot program to help patch viewLimits of bedGraph here.
• src/hg/oneShot/freen/freen.c
  • 1.94 lines changed: 69, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
  • 1.93 lines changed: 21, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/hg/oneShot/roundNewViewLimitsInRa/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work.
• src/hg/oneShot/roundNewViewLimitsInRa/roundNewViewLimitsInRa.c
  • 1.1 lines changed: 73, context: html, text, full: html, text
    Seems to work.
• src/hg/pslCDnaGenomeMatch/expected/mrna1.psl
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna12a.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna13b.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna13c.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrna5.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/mrnaDrop.psl
  • 1.2 lines changed: 399, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/pass1733.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/test15.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/testBQ.psl
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/expected/testDA9.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    updated test cases to fix strand[1] and new criteria
• src/hg/pslCDnaGenomeMatch/input/mrnaDrop.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    remove bad data
• src/hg/pslCDnaGenomeMatch/makefile
  • 1.12 lines changed: 20, context: html, text, full: html, text
    add -notAlignPenalty to reduce score for non-aligning bases. Fix strand bug with -passthru
• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
  • 1.28 lines changed: 72, context: html, text, full: html, text
    remove commented code
  • 1.27 lines changed: 132, context: html, text, full: html, text
    add -notAlignPenalty to reduce score for non-aligning bases. Fix strand bug with -passthru
• src/hg/qaPushQ/pushQ.as
  • 1.14 lines changed: 1, context: html, text, full: html, text
    enlarging user field at Bobs request
• src/hg/qaPushQ/pushQ.c
  • 1.13 lines changed: 0, context: html, text, full: html, text
    enlarging user field at Bobs request
• src/hg/qaPushQ/pushQ.h
  • 1.12 lines changed: 1, context: html, text, full: html, text
    enlarging user field at Bobs request
• src/hg/qaPushQ/pushQ.sql
  • 1.13 lines changed: 1, context: html, text, full: html, text
    enlarging user field at Bobs request
• src/hg/ratStuff/mafFilter/mafFilter.c
  • 1.15 lines changed: 22, context: html, text, full: html, text
    added option to filter mafs by species prefix
  • 1.14 lines changed: 1, context: html, text, full: html, text
    allow mafFilter -needComp to work on files produced by mafFrag that have species but not sequence in the name
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.25 lines changed: 14, context: html, text, full: html, text
    adding subsetLittleIds option where agp ok if all its ids in col 6 are found in the fasta files
• src/hg/utils/makefile
  • 1.18 lines changed: 2, context: html, text, full: html, text
    added missing wigBedToStep to make
  • 1.17 lines changed: 4, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/makefile
  • 1.1 lines changed: 25, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqGet.c
  • 1.2 lines changed: 14, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 274, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqVerInfo.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    fixed error detected in optimized compile
  • 1.1 lines changed: 152, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/refSeqVerInfo.h
  • 1.1 lines changed: 27, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 6, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.prot.fa
  • 1.1 lines changed: 20, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
  • 1.1 lines changed: 134, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.gp
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
  • 1.2 lines changed: 3, context: html, text, full: html, text
    added CDS to meta data
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.prot.fa
  • 1.1 lines changed: 17, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
  • 1.1 lines changed: 72, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/input/basic.acc
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/input/versioned.acc
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refSeqGet/tests/makefile
  • 1.1 lines changed: 35, context: html, text, full: html, text
    added program to get consistent versions of refseq data from database
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.9 lines changed: 3, context: html, text, full: html, text
    removed temporary variable no longer needed in transtion from name dataUrl to bigDataUrl
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSledgeHammer.pl
  • 1.5 lines changed: 3, context: html, text, full: html, text
    removed temporary variable no longer needed in transtion from name dataUrl to bigDataUrl
• src/hg/utils/scanSettings.pl
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Bug in determing parent from subTrack variable, may have "off" following name
  • 1.2 lines changed: 45, context: html, text, full: html, text
    Add some arguments to make it at least a little bit useful
  • 1.1 lines changed: 171, context: html, text, full: html, text
    Initial source of a scanner
• src/inc/bbiFile.h
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/inc/common.h
  • 1.163 lines changed: 14, context: html, text, full: html, text
    Making a couple of little functions inline.
  • 1.162 lines changed: 4, context: html, text, full: html, text
    Adding simplifyPathToDir
  • 1.161 lines changed: 2, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).
  • 1.160 lines changed: 1, context: html, text, full: html, text
    Added a couple const keywords for smoother interoperation with external code.
  • 1.159 lines changed: 6, context: html, text, full: html, text
    Adding sqlMatchLike
• src/inc/localmem.h
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Adding lmCloneStringZ
• src/inc/maf.h
  • 1.30 lines changed: 5, context: html, text, full: html, text
    added option to filter mafs by species prefix
• src/inc/obscure.h
  • 1.35 lines changed: 5, context: html, text, full: html, text
    Adding rangeFromMinMaxMeanStd
  • 1.34 lines changed: 6, context: html, text, full: html, text
    Adding 'hashThisEqThatLine.'
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Fixing missing commnt end.
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
• src/inc/portable.h
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/inc/ra.h
  • 1.7 lines changed: 12, context: html, text, full: html, text
    Adding a few new .ra parsing routines.
• src/inc/tokenizer.h
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Adding leadingSpaces field to tokenizer
• src/inc/udc.h
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Added udcParseUrlFull, which returns http auth portion instead of silently skipping it.
• src/index/indexfa/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/indexgl/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixali/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixword1/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixword3/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/makepgo/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/stToXao/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/lib/bbiRead.c
  • 1.17 lines changed: 8, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/lib/bigBed.c
  • 1.24 lines changed: 8, context: html, text, full: html, text
    Fixing bug in maxItem handling in bigBedIntervalQuery
• src/lib/bwgCreate.c
  • 1.22 lines changed: 80, context: html, text, full: html, text
    Getting rid of largely redundant bwgSectionWriteUnc
• src/lib/common.c
  • 1.140 lines changed: 20, context: html, text, full: html, text
    Making a couple of little functions inline.
  • 1.139 lines changed: 3, context: html, text, full: html, text
    Tiny bit more protection for findWordByDilimiter()
  • 1.138 lines changed: 10, context: html, text, full: html, text
    Adding simplifyPathToDir
  • 1.137 lines changed: 1, context: html, text, full: html, text
    Added a couple const keywords for smoother interoperation with external code.
• src/lib/localmem.c
  • 1.11 lines changed: 12, context: html, text, full: html, text
    Adding lmCloneStringZ
• src/lib/maf.c
  • 1.41 lines changed: 21, context: html, text, full: html, text
    added option to filter mafs by species prefix
• src/lib/makefile
  • 1.156 lines changed: 1, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
• src/lib/numObscure.c
  • 1.3 lines changed: 42, context: html, text, full: html, text
    Adding rangeIncludingZero logic to rangeFromMinMaxMeanStd in case when min/max/mean are the same.
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Adding rangeFromMinMaxMeanStd
  • 1.1 lines changed: 65, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
• src/lib/obscure.c
  • 1.52 lines changed: 61, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
  • 1.51 lines changed: 12, context: html, text, full: html, text
    Adding 'hashThisEqThatLine.'
  • 1.50 lines changed: 4, context: html, text, full: html, text
    Polishing routine that rounds ranges.
  • 1.49 lines changed: 59, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
• src/lib/osunix.c
  • 1.44 lines changed: 140, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/lib/ra.c
  • 1.14 lines changed: 60, context: html, text, full: html, text
    Adding a few new .ra parsing routines.
• src/lib/tokenizer.c
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Adding leadingSpaces field to tokenizer
• src/lib/udc.c
  • 1.30 lines changed: 19, context: html, text, full: html, text
    Added udcParseUrlFull, which returns http auth portion instead of silently skipping it.
  • 1.29 lines changed: 2, context: html, text, full: html, text
    Adding rcsid for version tracking with ident.
  • 1.28 lines changed: 4, context: html, text, full: html, text
    Fix: remember to close sockets if necessary in udcFileClose.
• src/lib/wildcmp.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).
  • 1.6 lines changed: 44, context: html, text, full: html, text
    Adding sqlMatchLike
• src/parasol/paraHub/paraHub.c
  • 1.132 lines changed: 9, context: html, text, full: html, text
    fixed incorrect usage message
• src/parasol/paraNode/paraNode.c
  • 1.82 lines changed: 24, context: html, text, full: html, text
    added option to allow setting arbitrary environment variable for jobs
• src/parasol/paraNodeStart/paraNodeStart.c
  • 1.15 lines changed: 12, context: html, text, full: html, text
    added option to allow setting arbitrary environment variable for jobs
• src/parasol/parasol/parasol.c
  • 1.48 lines changed: 7, context: html, text, full: html, text
    added an option to connect to a remote hub (for jobTree)
• src/product/ex.hg.conf
  • 1.19 lines changed: 10, context: html, text, full: html, text
    adding geographic allele frequency images options
  • 1.18 lines changed: 50, context: html, text, full: html, text
    Brought up to date on the occassion of losing the copy on genome-test
• src/shortReads/bwtMake/bananas.suffix
  • 1.2 lines changed: 52, context: html, text, full: html, text
    Commenting on bananas example.
• src/shortReads/bwtMake/bwtMake.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Tweaking size check to compile under 32 bit Mac OS.
• src/shortReads/itsaFind/itsaFind.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Commenting out some debugging statements.
• src/shortReads/itsaMake/itsaMake.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Improving comment.
• src/utils/ave/ave.c
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Previous standard deviation was incorrect, was not using N-1
• src/utils/bedClip/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding required -lz to link line.
• src/utils/bigWigSummary/bigWigSummary.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/utils/makefile
  • 1.76 lines changed: 1, context: html, text, full: html, text
    Adding bedClip to utilities build.
  • 1.75 lines changed: 1, context: html, text, full: html, text
    Adding raSqlQuery to makefile of parent.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.90 lines changed: 3, context: html, text, full: html, text
    v220 final build
• src/utils/raMerge/raMerge.c
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Adding -firstOnly option.
• src/utils/raSqlQuery/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding 'strict' option, to only put in ones where database table exists.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Starting work on raSqlQuery.
• src/utils/raSqlQuery/raRecord.c
  • 1.8 lines changed: 80, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Skipping over things inside parenthesis in count(*). Trimming spaces.
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.4 lines changed: 40, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Adding -addFile option.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixes to get to compile under Linux unstead of my laptop.
  • 1.1 lines changed: 61, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/raRecord.h
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Adding -addFile option.
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding raRecord.h
• src/utils/raSqlQuery/raSqlQuery.c
  • 1.24 lines changed: 5, context: html, text, full: html, text
    Fixing bug in track replacement by lower level tracks. Downgraded a verbose 2 to a verbose 3.
  • 1.23 lines changed: 66, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.22 lines changed: 56, context: html, text, full: html, text
    Making count statement work better with db=all and with from clauses.
  • 1.21 lines changed: 39, context: html, text, full: html, text
    Implementing from as file list.
  • 1.20 lines changed: 13, context: html, text, full: html, text
    Improving usage statement.
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Adding a little more error checking to command line.
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Adding a little more error checking to command line.
  • 1.17 lines changed: 12, context: html, text, full: html, text
    Adding 'strict' option, to only put in ones where database table exists.
  • 1.16 lines changed: 102, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.15 lines changed: 198, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.14 lines changed: 27, context: html, text, full: html, text
    Doing some stuff to cope with track names having additional fields after the first word.
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Fixing it so only prints file field once.
  • 1.12 lines changed: 29, context: html, text, full: html, text
    Adding -addFile option.
  • 1.11 lines changed: 119, context: html, text, full: html, text
    Adding parent,key,noInherit options and implementing inheritance.
  • 1.10 lines changed: 948, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Improving usage statement.
  • 1.8 lines changed: 41, context: html, text, full: html, text
    Adding parenthesis in expressions.
  • 1.7 lines changed: 115, context: html, text, full: html, text
    Adding 'or' and 'and'
  • 1.6 lines changed: 38, context: html, text, full: html, text
    Allowing like in where spec.
  • 1.5 lines changed: 44, context: html, text, full: html, text
    Making wildcards (other than the single ?) work in field specs.
  • 1.4 lines changed: 128, context: html, text, full: html, text
    Adding inequalities. Reducing debugging uglies to verboses.
  • 1.3 lines changed: 34, context: html, text, full: html, text
    Adding unary minus.
  • 1.2 lines changed: 221, context: html, text, full: html, text
    Adding casts to parse tree and evaluator so can have numeric as well as string types. Making floating point numbers parse.
  • 1.1 lines changed: 658, context: html, text, full: html, text
    Starting work on raSqlQuery.
• src/utils/raSqlQuery/rql.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Parsing out (and ignoring) optional from clause.
  • 1.1 lines changed: 98, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/rqlEval.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.1 lines changed: 286, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/rqlParse.c
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Implementing from as file list.
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Skipping over things inside parenthesis in count(*). Trimming spaces.
  • 1.6 lines changed: 20, context: html, text, full: html, text
    Parsing out (and ignoring) optional from clause.
  • 1.5 lines changed: 21, context: html, text, full: html, text
    Letting 'select count(*)' be a synonym for 'count'
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixes to get to compile under Linux unstead of my laptop.
  • 1.2 lines changed: 23, context: html, text, full: html, text
    Adding logical not
  • 1.1 lines changed: 572, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/test.ra
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Adding test set.
• src/utils/raSqlQuery/test2.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Adding parent,key,noInherit options and implementing inheritance.
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Adding test set.
• src/utils/wigAsciiToBinary/wiggleFAQ.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    change autoScaleDefault to be only autoScale
  • 1.2 lines changed: 4, context: html, text, full: html, text
    change defaultViewLimits to viewLimits

• lines changed: 23909
• files changed: 436