CVS changes by file

review to branch (2009-06-30 to 2009-07-07) v210

• src/hg/archaeStuff/data/Genome-info-euk
  • 1.17 lines changed: 13, context: html, text, full: html, text
    add hg19
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.36 lines changed: 2, context: html, text, full: html, text
    fix bug of replacing ORG_DB on description page
• src/hg/autoSql/autoSql.c
  • 1.38 lines changed: 10, context: html, text, full: html, text
    adjust enum/set values to be valid C indentifiers
• src/hg/autoSql/makefile
  • 1.16 lines changed: 6, context: html, text, full: html, text
    adjust enum/set values to be valid C indentifiers
• src/hg/encode/DAFs/CshlLongRnaSeq.daf
  • 1.1 lines changed: 41, context: html, text, full: html, text
    Long RNA metadata files for CSHL
• src/hg/encode/DAFs/CshlLongRnaSeq.ddf
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Long RNA metadata files for CSHL
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.119 lines changed: 8, context: html, text, full: html, text
    added new field restrictionEnzyme
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.18 lines changed: 5, context: html, text, full: html, text
    added new field restrictionEnzyme
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    change Myers wranglerEmail to braney
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.186 lines changed: 1, context: html, text, full: html, text
    submittedDataVersion=Vn needed to be added to metadata
• src/hg/hgTables/filterFields.c
  • 1.78 lines changed: 116, context: html, text, full: html, text
    Fixing nearly empty filter page on bigBed custom tracks.
• src/hg/hgTracks/cds.c
  • 1.103 lines changed: 2, context: html, text, full: html, text
    In maybeGetSeqUpper, no need to cloneString the third arg of newDnaSeq (code review - thanks Tim).
• src/hg/hgTracks/hgTracks.c
  • 1.1580 lines changed: 6, context: html, text, full: html, text
    Very minor work towards making the imgBox portal. Mostly just want to check in some format changes before too much dust gathers
• src/hg/hgTracks/imageV2.c
  • 1.4 lines changed: 194, context: html, text, full: html, text
    Very minor work towards making the imgBox portal. Mostly just want to check in some format changes before too much dust gathers
• src/hg/hgTracks/imageV2.h
  • 1.3 lines changed: 99, context: html, text, full: html, text
    Very minor work towards making the imgBox portal. Mostly just want to check in some format changes before too much dust gathers
• src/hg/hgTracks/simpleTracks.c
  • 1.90 lines changed: 4, context: html, text, full: html, text
    Add trackDb setting for minimum gray level, corresponding to trackUi min gray level dropdown
  • 1.89 lines changed: 3, context: html, text, full: html, text
    Added filterBy using 'score' so that ENCODE NHGRI BiPs can filter on annotations
• src/hg/inc/gbSeq.h
  • 1.1 lines changed: 81, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/inc/hCommon.h
  • 1.25 lines changed: 4, context: html, text, full: html, text
    deleted no longer needed function
• src/hg/inc/hui.h
  • 1.133 lines changed: 11, context: html, text, full: html, text
    Added vaule|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips
• src/hg/inc/refSeqStatus.h
  • 1.2 lines changed: 42, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/inc/versionInfo.h
  • 1.150 lines changed: 1, context: html, text, full: html, text
    "New version number v210"
• src/hg/lib/encode/wgEncodeGencodeClasses.as
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Inital check-in of Encode Gencode Classes table
• src/hg/lib/encode/wgEncodeGencodeClasses.sql
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Inital check-in of Encode Gencode Classes table
• src/hg/lib/gbSeq.as
  • 1.1 lines changed: 14, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/gbSeq.c
  • 1.1 lines changed: 168, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/gbSeq.sql
  • 1.1 lines changed: 19, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/genbankTables.as
  • 1.6 lines changed: 14, context: html, text, full: html, text
    removed gbSeq, as it is in it's own file
• src/hg/lib/hui.c
  • 1.221 lines changed: 3, context: html, text, full: html, text
    Add trackDb setting for minimum gray level, corresponding to trackUi min gray level dropdown
  • 1.220 lines changed: 2, context: html, text, full: html, text
    Removed an extra .. from a help link
  • 1.219 lines changed: 68, context: html, text, full: html, text
    Added value|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips
  • 1.218 lines changed: 33, context: html, text, full: html, text
    make sure hgPal is in sync with composite multiz tracks
• src/hg/lib/makefile
  • 1.391 lines changed: 1, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/pal.c
  • 1.14 lines changed: 7, context: html, text, full: html, text
    make sure hgPal is in sync with composite multiz tracks
• src/hg/lib/refSeqStatus.as
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/refSeqStatus.c
  • 1.4 lines changed: 39, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/lib/refSeqStatus.sql
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added some .h files for genbank tables
• src/hg/makeDb/doc/canFam2.txt
  • 1.20 lines changed: 123, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/equCab2.txt
  • 1.26 lines changed: 141, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/galGal3.txt
  • 1.28 lines changed: 51, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/hg18.txt
  • 1.367 lines changed: 57, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/mm9.txt
  • 1.101 lines changed: 54, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/monDom5.txt
  • 1.11 lines changed: 63, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/ornAna1.txt
  • 1.25 lines changed: 18, context: html, text, full: html, text
    Rerun all the equCab2 chains and nets to clean up problems
• src/hg/makeDb/doc/sacCer2.txt
  • 1.10 lines changed: 27, context: html, text, full: html, text
    Making upstream maf files from the 7-way alignment
  • 1.9 lines changed: 2, context: html, text, full: html, text
    oops. munged the rename
• src/hg/makeDb/genbank/etc/dbload
  • 1.29 lines changed: 3, context: html, text, full: html, text
    don't adjust core limit
• src/hg/makeDb/genbank/src/inc/gbDefs.h
  • 1.9 lines changed: 1, context: html, text, full: html, text
    added program to quickly validate refseq tables
• src/hg/makeDb/genbank/src/makefile
  • 1.10 lines changed: 1, context: html, text, full: html, text
    added program to quickly validate refseq tables
• src/hg/makeDb/trackDb/README
  • 1.82 lines changed: 2, context: html, text, full: html, text
    Add trackDb setting for minimum gray level, corresponding to trackUi min gray level dropdown
• src/hg/makeDb/trackDb/chainNet.html
  • 1.1 lines changed: 155, context: html, text, full: html, text
    Adding Horse chains and nets as a composite
• src/hg/makeDb/trackDb/chicken/priority.ra
  • 1.8 lines changed: 6, context: html, text, full: html, text
    priority for human and horse chainNet composites
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.11 lines changed: 14, context: html, text, full: html, text
    EquCab2 track moved up to the composite
  • 1.10 lines changed: 4, context: html, text, full: html, text
    priority for human and horse chainNet composites
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.37 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.36 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.11 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.31 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.30 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
• src/hg/makeDb/trackDb/dog/priority.ra
  • 1.6 lines changed: 7, context: html, text, full: html, text
    Fixup equCab2 chain net priorities and overrides for hg19 chain net composite
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Fixup equCab2 chain net priorities and overrides for hg19 chain net composite
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.405 lines changed: 10, context: html, text, full: html, text
    Cleanup for Mapability. BiPs now use new 'filterBy score'.
  • 1.404 lines changed: 1, context: html, text, full: html, text
    Use new setting to set minimum gray level for Affy RNA transfrags
  • 1.403 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
  • 1.402 lines changed: 1, context: html, text, full: html, text
    Laura Elnotski wishes BiP to be Bi-Pro
  • 1.401 lines changed: 1, context: html, text, full: html, text
    Add dataVersion to Affy RNA composite
  • 1.400 lines changed: 2, context: html, text, full: html, text
    changed longlable to provisional release on some HudAlph tracks
  • 1.399 lines changed: 88, context: html, text, full: html, text
    used removeAlpha to remove release alpha lines as appropriate from Affy RNA tracks (thanks Brooke)
  • 1.398 lines changed: 270, context: html, text, full: html, text
    Snyder wanted some cell line order changes
  • 1.397 lines changed: 4, context: html, text, full: html, text
    More label fixups for Affy RNA
  • 1.396 lines changed: 1, context: html, text, full: html, text
    Label fixup
  • 1.395 lines changed: 8, context: html, text, full: html, text
    Color up new Affy RNA tracks
  • 1.394 lines changed: 18, context: html, text, full: html, text
    Remove obsolete priorities from Affy RNA
  • 1.393 lines changed: 19, context: html, text, full: html, text
    Correct errors in Affy RNA track labels, and update freeze date
  • 1.392 lines changed: 943, context: html, text, full: html, text
    Additions to UW ENCODE tracks.
  • 1.391 lines changed: 1, context: html, text, full: html, text
    Rosetta uniqueness should be consistent
  • 1.390 lines changed: 25, context: html, text, full: html, text
    Moving Rosetta uniqueness track into Mapability
  • 1.389 lines changed: 6, context: html, text, full: html, text
    Also collapsed HepG2 and HepG2b into a single column.
  • 1.388 lines changed: 28, context: html, text, full: html, text
    Collapsed K562 and K562b into a single column. Not the best solution, but neither was 2 columns quite right.
  • 1.387 lines changed: 299, context: html, text, full: html, text
    Resubmitted Yale/K562 peaks, input. Fixed some metadata, standardized ChIP-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.14 lines changed: 22, context: html, text, full: html, text
    fixed citations and typo.
  • 1.13 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqProv.html
  • 1.1 lines changed: 135, context: html, text, full: html, text
    adding provision html file for a HudsAlpha track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.12 lines changed: 10, context: html, text, full: html, text
    Cleaned up.
  • 1.11 lines changed: 29, context: html, text, full: html, text
    Moving Rosetta uniqueness track into Mapability
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.15 lines changed: 6, context: html, text, full: html, text
    made wording consistent and correct
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.33 lines changed: 8, context: html, text, full: html, text
    turned on some primate net defaults so the primate chain/net track is not empty when first turned on
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.465 lines changed: 18, context: html, text, full: html, text
    Moving Rosetta uniqueness track into Mapability
• src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/Diurnal.html
  • 1.1 lines changed: 210, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/EMSeffects.html
  • 1.1 lines changed: 72, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/FeSO4Time.html
  • 1.1 lines changed: 26, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/FeSO4stress.html
  • 1.1 lines changed: 12, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/FiveODLightSensitivity.html
  • 1.1 lines changed: 88, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/GTFchip.html
  • 1.1 lines changed: 116, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/GammaIrradiation.html
  • 1.1 lines changed: 106, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/H2O2effects.html
  • 1.1 lines changed: 72, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/MnSO4Stress.html
  • 1.1 lines changed: 10, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/NiSO4Stress.html
  • 1.1 lines changed: 12, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/OxygenResponse.html
  • 1.1 lines changed: 124, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/OxygenResponse2.html
  • 1.1 lines changed: 40, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/SmallODLightSensitivity.html
  • 1.1 lines changed: 76, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/TranscriptionFactors.html
  • 1.1 lines changed: 360, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/TransitionMetal.html
  • 1.1 lines changed: 194, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/UVradiation.html
  • 1.1 lines changed: 53, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/ZnSO4Stress.html
  • 1.1 lines changed: 10, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/description.html
  • 1.10 lines changed: 83, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.17 lines changed: 131, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/metaSedu/FerrSulf.html
  • 1.1 lines changed: 51, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/metaSedu/trackDb.ra
  • 1.9 lines changed: 14, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/methJann1/Barophilicgrowth.html
  • 1.1 lines changed: 45, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/methJann1/HeatPressureShock.html
  • 1.1 lines changed: 70, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/methJann1/trackDb.ra
  • 1.12 lines changed: 28, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
  • 1.53 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroCali1/trackDb.ra
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/sulSol1/AerobicGrowth.html
  • 1.1 lines changed: 16, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/sulSol1/STIVinfect.html
  • 1.1 lines changed: 75, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/sulSol1/trackDb.ra
  • 1.19 lines changed: 27, context: html, text, full: html, text
    add microarray tracks created by Andrew Holmes
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.54 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.53 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
  • 1.52 lines changed: 15, context: html, text, full: html, text
    release alpha/beta cleanup
• src/hg/makeDb/trackDb/mouse/priority.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    horse and human chainNet overrides
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.154 lines changed: 10, context: html, text, full: html, text
    horse and human chainNet overrides
• src/hg/makeDb/trackDb/nscanGene.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Minor reference formatting
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.29 lines changed: 10, context: html, text, full: html, text
    overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/platypus/priority.ra
  • 1.2 lines changed: 7, context: html, text, full: html, text
    No longer need the priority here, it is in the trackDb.ra now
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.37 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.36 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.42 lines changed: 2, context: html, text, full: html, text
    Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • 1.41 lines changed: 2, context: html, text, full: html, text
    ENCODE NHGRI Bidirectional promoters has no '-'.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.517 lines changed: 211, context: html, text, full: html, text
    Composite chain/net tracks for equCab2 release, chicken, platypus, opossum, human, mouse, dog
  • 1.516 lines changed: 39, context: html, text, full: html, text
    Adding Horse chains and nets as a composite
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • 1.3 lines changed: 55, context: html, text, full: html, text
    Last minute addition of another reference.
• src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caeRem3/description.html
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caeRem3/gap.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caeRem3/gold.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/cb1/description.html
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Fixed link to data use policy.
• src/hg/makeDb/trackDb/worm/cb2/description.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed link to data use policy.
• src/hg/makeDb/trackDb/worm/cb3/description.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed link to data use policy.
• src/hg/pslCDnaFilter/algo.txt
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed typo in help
  • 1.2 lines changed: 3, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/cDnaAligns.c
  • 1.19 lines changed: 10, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/cDnaAligns.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/cDnaStats.c
  • 1.2 lines changed: 40, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/cDnaStats.h
  • 1.2 lines changed: 15, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/overlapFilter.c
  • 1.8 lines changed: 91, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
  • 1.7 lines changed: 2, context: html, text, full: html, text
    clairfed documentation
• src/hg/pslCDnaFilter/overlapFilter.h
  • 1.5 lines changed: 8, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
  • 1.4 lines changed: 2, context: html, text, full: html, text
    clairfed documentation
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • 1.21 lines changed: 63, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/globalBestTest/filt.out
  • 1.3 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/hapLocalXenoTest/filt.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/localBestTest/filt.out
  • 1.3 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/minAlnSizeTest/filt.out
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/nonRepMismatchTest/filt.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/nonRepSizeTest/filt.out
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/noopTest/filt.out
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/noopTest/weird.psl
  • 1.2 lines changed: 9, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/overlapTest/filt.out
  • 1.9 lines changed: 4, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/overlapTest/weird.psl
  • 1.5 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/expected/repMatchTest/filt.out
  • 1.7 lines changed: 2, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/tests/makefile
  • 1.13 lines changed: 9, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
• src/hg/pslCDnaFilter/usage.txt
  • 1.11 lines changed: 2, context: html, text, full: html, text
    fixed typo in help
  • 1.10 lines changed: 9, context: html, text, full: html, text
    added option to drop weird overlapps independent of other filtering
  • 1.9 lines changed: 2, context: html, text, full: html, text
    clairfed documentation
• src/index/bptForTwoBit/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Needs SOCKETLIB for build on solaris
• src/index/bptLookupStringToBits64/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Needs SOCKETLIB for build on Solaris
• src/index/bptMakeStringToBits64/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Needs SOCKETLIB for build on Solaris
• src/lib/cheapcgi.c
  • 1.124 lines changed: 4, context: html, text, full: html, text
    Don't printf something that might be NULL -- it segv's on Solaris.
• src/parasol/paraHub/makefile
  • 1.20 lines changed: 1, context: html, text, full: html, text
    fixed library list so SSL can be included
• src/utils/bedToBigBed/makefile
  • 1.5 lines changed: 14, context: html, text, full: html, text
    dding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/bigBedSummary/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    dding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/bigBedToBed/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/bigWigSummary/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/bigWigToBedGraph/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/faToTwoBit/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/findMotif/findMotif.c
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Fixing a gap confusion bug
• src/utils/findMotif/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/makefile
  • 1.72 lines changed: 1, context: html, text, full: html, text
    dding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/newProg/newProg.c
  • 1.28 lines changed: 2, context: html, text, full: html, text
    When adding libs to L, use += not = so we keep the -lssl from inc/common.mk when USE_SSL=1.
• src/utils/pslToPslx/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/qa/chainNetTrio.csh
  • 1.9 lines changed: 1, context: html, text, full: html, text
    corrected some info on usage statement
• src/utils/qa/findBlatServer.csh
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Changed single quotes to double quotes so that sqlbeta variable gets interpreted.
• src/utils/qa/igtc.csh
  • 1.23 lines changed: 3, context: html, text, full: html, text
    small changes
• src/utils/qa/removeAlphas
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Added a few more details to the usage statement.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.66 lines changed: 3, context: html, text, full: html, text
    v210 final build
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • 1.16 lines changed: 10, context: html, text, full: html, text
    Changed push request notes.
• src/utils/twoBitInfo/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/twoBitToFa/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/udcCleanup/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/utils/wigToBigWig/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris
• src/weblet/bottleneck/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Needs SOCKETLIB for build on solaris

• lines changed: 6634
• files changed: 165