CVS changes by file

review to branch (2009-06-16 to 2009-06-23) v209

• src/hg/archaeStuff/data/Genome-info-euk
  • 1.16 lines changed: 4, context: html, text, full: html, text
    change mt2 to mt3
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.4 lines changed: 2, context: html, text, full: html, text
    add Josue's short protein track
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.14 lines changed: 37, context: html, text, full: html, text
    Moved sub metadataLineToArrays to Encode.pm so that doEncodeValidate.pl can also use it
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.66 lines changed: 4, context: html, text, full: html, text
    Respond to request from MarkD to correct hostname
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.117 lines changed: 3, context: html, text, full: html, text
    Rename cell type for more specificity
  • 1.116 lines changed: 39, context: html, text, full: html, text
    Added 3 new tier 3s for Stam lab
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.17 lines changed: 5, context: html, text, full: html, text
    Added dataVersion for the DAF
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.184 lines changed: 1, context: html, text, full: html, text
    That was a stupid error
  • 1.183 lines changed: 58, context: html, text, full: html, text
    Trying to get old metadata for new submissions
• src/hg/encode/encodeValidate/test/input/methylseq/HudsonAlphaMethylSeq.DAF
  • 1.2 lines changed: 5, context: html, text, full: html, text
    add RawData
• src/hg/encode/encodeValidate/test/input/methylseq/HudsonAlphaMethylSeq.DDF
  • 1.5 lines changed: 2, context: html, text, full: html, text
    add RawData
• src/hg/encode/validateFiles/validateFiles.c
  • 1.18 lines changed: 2, context: html, text, full: html, text
    bed files allow comment lines
• src/hg/hgGene/links.c
  • 1.38 lines changed: 0, context: html, text, full: html, text
    Fixup background color on Links Out table when only one row of links ...
• src/hg/hgTables/filterFields.c
  • 1.77 lines changed: 16, context: html, text, full: html, text
    When selecting fields for output, automatically include any tables specified in trackDb setting defaultLinkedTables.
• src/hg/hgTables/joining.c
  • 1.56 lines changed: 2, context: html, text, full: html, text
    Added NULL check -- this can happen when a trackDb setting specifies a table that isn't properly linked in all.joiner.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.494 lines changed: 1, context: html, text, full: html, text
    scale bar defaults to on, just like hgTracks.
  • 1.493 lines changed: 6, context: html, text, full: html, text
    Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s).
• src/hg/hgTracks/config.c
  • 1.80 lines changed: 11, context: html, text, full: html, text
    add dragZoomingConfig
• src/hg/hgTracks/hgTracks.c
  • 1.1573 lines changed: 2, context: html, text, full: html, text
    use dragZoomingConfig; currently defaults to off for safari and chrome b/c drag-and-zoom doesn't work under WebKit; make superTrackHasVisibleMembers non-static
• src/hg/hgTracks/hgTracks.h
  • 1.183 lines changed: 8, context: html, text, full: html, text
    add dragZoomingConfig
• src/hg/hgTracks/simpleTracks.c
  • 1.84 lines changed: 9, context: html, text, full: html, text
    getting wider use of sorted genepreds including knownGene
• src/hg/hgc/bigBedClick.c
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Removing some debugging code.
• src/hg/hgc/hgc.c
  • 1.1557 lines changed: 4, context: html, text, full: html, text
    Added note that HDGP geographical allele images may show alleles from the - strand (thanks David).
  • 1.1556 lines changed: 6, context: html, text, full: html, text
    Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s).
• src/hg/inc/versionInfo.h
  • 1.149 lines changed: 1, context: html, text, full: html, text
    "New version number v209"
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.68 lines changed: 1, context: html, text, full: html, text
    fix bug: missing last feature value in output file
  • 1.67 lines changed: 77, context: html, text, full: html, text
    add feature value output to file, fix bug in feature summary view
• src/hg/makeDb/doc/danRer6.txt
  • 1.1 lines changed: 118, context: html, text, full: html, text
    start zv8
• src/hg/makeDb/doc/hg19.txt
  • 1.27 lines changed: 8, context: html, text, full: html, text
    Need to load exoniphy manually, it seems to have different columns in it ?
  • 1.26 lines changed: 695, context: html, text, full: html, text
    Cytobands done, Venter Poodle chain/net done, starting 46-way conservation, exoniphy lifted from hg18, liftOver to hg18 done.
• src/hg/makeDb/doc/sacCer2.txt
  • 1.7 lines changed: 6, context: html, text, full: html, text
    added record of RENAME of table knownBlastTab to sgdBlastTab so GS can use it. thanks katrina
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh
  • 1.2 lines changed: 28, context: html, text, full: html, text
    Have proceeded through the first cluster job OK without CCDS genes
  • 1.1 lines changed: 1121, context: html, text, full: html, text
    Beginning to work through this script to get it ready for UCSC gene build
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.113 lines changed: 8, context: html, text, full: html, text
    added bug
  • 1.112 lines changed: 2, context: html, text, full: html, text
    added bug
• src/hg/makeDb/genbank/etc/align-genbank
  • 1.36 lines changed: 3, context: html, text, full: html, text
    don't allow core dumps
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.79 lines changed: 1, context: html, text, full: html, text
    fix cell line name
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.53 lines changed: 1, context: html, text, full: html, text
    fixed dereference of NULL in error check
• src/hg/makeDb/schema/all.joiner
  • 1.720 lines changed: 1, context: html, text, full: html, text
    Added mm6 back to mm -- it is still on hgwdev.
• src/hg/makeDb/trackDb/README
  • 1.79 lines changed: 2, context: html, text, full: html, text
    Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s).
  • 1.78 lines changed: 2, context: html, text, full: html, text
    Added new setting defaultLinkedTables.
• src/hg/makeDb/trackDb/affyExonTissues.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Changing credits to reflect upcoming publication.
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Changing credits and refs to reflect upcoming publication.
• src/hg/makeDb/trackDb/ccdsGene.html
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Added CCDS paper reference.
• src/hg/makeDb/trackDb/chainPanTro2.html
  • 1.4 lines changed: 5, context: html, text, full: html, text
    tweaked pubMed format per ann
• src/hg/makeDb/trackDb/human/cytoBand.html
  • 1.13 lines changed: 2, context: html, text, full: html, text
    tweaked pubMed format per ann
• src/hg/makeDb/trackDb/human/hg15/trackDb.ra
  • 1.85 lines changed: 4, context: html, text, full: html, text
    Add override labels for knownGene (now UCSC Genes at top level).
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.573 lines changed: 11, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.425 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/human/hg18/encodeUCDavisChip.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Changed crosslink to cross-link to be consistent everywhere.
• src/hg/makeDb/trackDb/human/hg18/encodeUcDavisChipHits.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Changed crosslink to cross-link to be consistent everywhere.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.398 lines changed: 14, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
  • 1.397 lines changed: 1, context: html, text, full: html, text
    Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.374 lines changed: 17, context: html, text, full: html, text
    fixed up labels and #75
  • 1.373 lines changed: 19, context: html, text, full: html, text
    addign missing Filtered tables due to metadata problem
  • 1.372 lines changed: 20, context: html, text, full: html, text
    fixing Gm12878NucleusTotal to be Gm12878NucleusLongpolya And, reloading *Transfrags as the tables were missing
  • 1.371 lines changed: 81, context: html, text, full: html, text
    new affy tracks for #375 #376
  • 1.370 lines changed: 1, context: html, text, full: html, text
    Fix label
  • 1.369 lines changed: 1, context: html, text, full: html, text
    Reverted to allowing viewing negative signal on Affy RNA as it is explained in the description
  • 1.368 lines changed: 79, context: html, text, full: html, text
    Add CSHL to long labels of Affy RNA track, by request of submitter
  • 1.367 lines changed: 1, context: html, text, full: html, text
    Disallow negative signal viewing on Affy RNA , by request of Carrie Davis
  • 1.366 lines changed: 3, context: html, text, full: html, text
    Tune defaults for Affy RNA
  • 1.365 lines changed: 4, context: html, text, full: html, text
    Terry had one more adjustment
  • 1.364 lines changed: 10, context: html, text, full: html, text
    Added wgEncodeUncFAIREseqBaseOverlapSignalK562 back in
  • 1.363 lines changed: 6, context: html, text, full: html, text
    Correct whacked cell type from mass edit
  • 1.362 lines changed: 10, context: html, text, full: html, text
    Temporarily remove K562/FAIRE/Signal BO to reload it
  • 1.361 lines changed: 240, context: html, text, full: html, text
    1. Change Keratinocyte term to NHEK. 2. Readability mods to Affy RNA labels
  • 1.360 lines changed: 2, context: html, text, full: html, text
    Updates to track labels
  • 1.359 lines changed: 20, context: html, text, full: html, text
    Open Chromatin short labels of GM12878 cannot be abreviated to GM128.
  • 1.358 lines changed: 7, context: html, text, full: html, text
    Someone finally had the sense to point out that the name 'Excludable regions' was a lemon
  • 1.357 lines changed: 3, context: html, text, full: html, text
    More twiddling... Actually fixing some of my mistakes with the last check-in
  • 1.356 lines changed: 73, context: html, text, full: html, text
    More adjustments for Terry's Open Chromatin
  • 1.355 lines changed: 29, context: html, text, full: html, text
    Terry's signal viewLimit defaults
  • 1.354 lines changed: 10, context: html, text, full: html, text
    Added release alpha back to Open Chromatin raw signal tracks.
  • 1.353 lines changed: 58, context: html, text, full: html, text
    Removed release alphas for initial release of Open Chromatin track.
  • 1.352 lines changed: 9, context: html, text, full: html, text
    Set Vishy Iyer's default viewLimits for ChIP experiments
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.12 lines changed: 33, context: html, text, full: html, text
    Changes after feedback from Carrie Davis
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Changed crosslink to cross-link to be consistent everywhere.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Forgot a line break.
  • 1.19 lines changed: 51, context: html, text, full: html, text
    More edits after consulting Tim and Kate. Added a reference and links to protocols.
  • 1.18 lines changed: 32, context: html, text, full: html, text
    Edits to References section.
  • 1.17 lines changed: 31, context: html, text, full: html, text
    Lots of minor grammar/punctuation/consistency edits. Put Credits in a list. Made quotes html-friendly.
  • 1.16 lines changed: 167, context: html, text, full: html, text
    Whitespace changes.
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Someone finally had the sense to point out that the name 'Excludable regions' was a lemon
  • 1.14 lines changed: 4, context: html, text, full: html, text
    More twiddling... Actually fixing some of my mistakes with the last check-in
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Renamed Signal tracks on Terry's request
  • 1.12 lines changed: 27, context: html, text, full: html, text
    Terry requested some changes which recommend that the user turns on auto-scale for signals
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeDnase.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Changed crosslink to cross-link to be consistent everywhere.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Minor edits to ENCODE pages for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Minor edits to ENCODE pages for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Minor edits to ENCODE pages for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Someone finally had the sense to point out that the name 'Excludable regions' was a lemon
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Terry finally weighs in on 'Duke Excludable' regions description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Minor edits to ENCODE pages for consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
  • 1.1 lines changed: 41, context: html, text, full: html, text
    First draft UW Exon Arrays description.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Minor edits to ENCODE pages for consistency
  • 1.1 lines changed: 57, context: html, text, full: html, text
    First cut of the UW ChIP-seq description. Missing is the bit about antibodies because the table originally only listed one. Also, no track configuration stuff. And the overview section might be a bit on the technical side... in any case, it's in.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.32 lines changed: 8, context: html, text, full: html, text
    added nscanGene
  • 1.31 lines changed: 170, context: html, text, full: html, text
    Turning on first look at 46-way alignment
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Fixed termRegex for ctgPos2.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.464 lines changed: 1, context: html, text, full: html, text
    Moved the uniqueness track from the variation to the sequencing group
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.76 lines changed: 36, context: html, text, full: html, text
    add Josue's short protein track
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Updated links to WUSTL.
• src/hg/makeDb/trackDb/mouse/igtc.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Changed tigem link to location to which it was being redirected.
• src/hg/makeDb/trackDb/mouse/mm6/trackDb.ra
  • 1.53 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.55 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.55 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.50 lines changed: 27, context: html, text, full: html, text
    Removed local knownGene definition (duplicate of top level now).
• src/hg/makeDb/trackDb/netPanTro2.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    tweaked pubMed format per ann
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • 1.60 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.35 lines changed: 12, context: html, text, full: html, text
    Convert knownGene to override, to simplify and to inherit new top-level settings.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.39 lines changed: 2, context: html, text, full: html, text
    Changed priority of SGD Gene and SGD Other so that they are first and second in their track group
• src/hg/makeDb/trackDb/snp128.html
  • 1.12 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
  • 1.11 lines changed: 1, context: html, text, full: html, text
    removed capitals on Single Nuc Polymorphism
  • 1.10 lines changed: 3, context: html, text, full: html, text
    expanded description of track jsut a little. explaining Simple Nuc Polymorphism
• src/hg/makeDb/trackDb/snp129.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
  • 1.9 lines changed: 1, context: html, text, full: html, text
    removed capitals on Single Nuc Polymorphism
  • 1.8 lines changed: 3, context: html, text, full: html, text
    expanded description of track jsut a little. explaining Simple Nuc Polymorphism
  • 1.7 lines changed: 10, context: html, text, full: html, text
    removed some comments about comparing to previous versions
• src/hg/makeDb/trackDb/snp130.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added a little whitespace at the bottom
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added clarification for meaning of cds-reference / "Reference (coding)".
  • 1.4 lines changed: 1, context: html, text, full: html, text
    removed capitals on Single Nuc Polymorphism
  • 1.3 lines changed: 3, context: html, text, full: html, text
    expanded description of track jsut a little. explaining Simple Nuc Polymorphism
  • 1.2 lines changed: 10, context: html, text, full: html, text
    removed some comments about comparing to previous versions
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.515 lines changed: 2, context: html, text, full: html, text
    Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s).
  • 1.514 lines changed: 2, context: html, text, full: html, text
    Make UCSC Genes the default label for knownGene going forward.
  • 1.513 lines changed: 1, context: html, text, full: html, text
    Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables.
  • 1.512 lines changed: 3, context: html, text, full: html, text
    hgFindSpec tweaks: for the more restrictive stsMapAliasMrnaAcc search, don't require that all aliases match the termRegex. Broaden sgpGene and geneid termRegexes to accomodate hg19.
• src/hg/makefile
  • 1.152 lines changed: 1, context: html, text, full: html, text
    bedSplitOnChrom should be on the build list, used in UCSC gene production
• src/hg/near/hgNear/hgNearData/S_cerevisiae/sgdAbundance.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    commented out reference to main GFP site because link is broken
  • 1.2 lines changed: 5, context: html, text, full: html, text
    added a bit more explanation of just what this is. and changed broken link to paper. thanks, katrina
• src/hg/utils/automation/Encode.pm
  • 1.43 lines changed: 36, context: html, text, full: html, text
    I forgot to check this in earlier. Moved metadataLinesToArrays from encodeDownloadsPage.pl to lib so that it could be called by doEnocodeValidate.pl
• src/inc/bbiFile.h
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Updating comments to more closely reflect code.
• src/inc/bigBed.h
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Updating comments to more closely reflect code.
• src/inc/bigWig.h
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Updating comments to more closely reflect code.
• src/inc/cheapcgi.h
  • 1.67 lines changed: 3, context: html, text, full: html, text
    add cgiUserAgent
• src/inc/memgfx.h
  • 1.24 lines changed: 57, context: html, text, full: html, text
    added RGB->HSL/HSV->RGB conversion and transformation code, plus test cases in colorConv program
• src/lib/cheapcgi.c
  • 1.123 lines changed: 6, context: html, text, full: html, text
    add cgiUserAgent
• src/lib/memgfx.c
  • 1.51 lines changed: 2, context: html, text, full: html, text
    remove unnecesary dependence on math:floor()
  • 1.50 lines changed: 1, context: html, text, full: html, text
    floor is in math.h, dont know why it builds for me but not the nightly build
  • 1.49 lines changed: 254, context: html, text, full: html, text
    added RGB->HSL/HSV->RGB conversion and transformation code, plus test cases in colorConv program
• src/test/buildTableDescriptions.pl
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Yet another duplicate to ignore.
• src/utils/bedToBigBed/itemRgb.as
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Adding an itemRgb test example
• src/utils/bedToBigBed/itemRgb.bed
  • 1.2 lines changed: 0, context: html, text, full: html, text
    The spaces need to be tabs since that is what comes out of bigBedToBed
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Adding an itemRgb test example
• src/utils/qa/makefile
  • 1.109 lines changed: 1, context: html, text, full: html, text
    Added removeAlphas.
• src/utils/qa/removeAlphas
  • 1.1 lines changed: 35, context: html, text, full: html, text
    Initial commit. Thanks, markd!
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.64 lines changed: 3, context: html, text, full: html, text
    v209 final build

• lines changed: 4371
• files changed: 87