CVS changes by file

branch to review (2009-06-09 to 2009-06-16) v208

• src/hg/encode/encodeValidate/config/cv.ra
  • 1.115 lines changed: 1, context: html, text, full: html, text
    expand description for NHEK
  • 1.114 lines changed: 2, context: html, text, full: html, text
    Lonza web site has changed
  • 1.113 lines changed: 8, context: html, text, full: html, text
    Added E2F6 antibody for Yale
  • 1.112 lines changed: 32, context: html, text, full: html, text
    Added K562b and HepG2b alternate cell lines because Yale and UCDavis can't agree
• src/hg/hgGene/hgGene.c
  • 1.115 lines changed: 8, context: html, text, full: html, text
    Prevent stack dump in case of stoopid invocation (googlebots).
• src/hg/hgNotYet/hgNotYet.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Added logic for GISAID.
• src/hg/hgSession/hgSession.c
  • 1.51 lines changed: 44, context: html, text, full: html, text
    Merged some duplicate notification messages about custom tracks and blat results when creating a session -- Thanks Ann.
• src/hg/hgTables/hgTables.c
  • 1.187 lines changed: 15, context: html, text, full: html, text
    Enabled doValueRange and doValueHistogram for GSID and GISAID.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.492 lines changed: 1, context: html, text, full: html, text
    Fixup chainCfgUi to work properly on split table names
• src/hg/hgTracks/bedTrack.c
  • 1.14 lines changed: 13, context: html, text, full: html, text
    fixing - strandness problem with paired tag align data
• src/hg/hgTracks/cds.c
  • 1.100 lines changed: 12, context: html, text, full: html, text
    Some code for codons smaller than 3 bases was erroneously applied to noncoding blocks smaller than 3 bases.
• src/hg/hgTracks/hgTracks.c
  • 1.1572 lines changed: 2, context: html, text, full: html, text
    Disable hgGateway top bar link for GISAID.
  • 1.1571 lines changed: 3, context: html, text, full: html, text
    Minor updates for GISAID.
  • 1.1570 lines changed: 1, context: html, text, full: html, text
    turned on scalebar by default
• src/hg/hgTracks/netTrack.c
  • 1.26 lines changed: 29, context: html, text, full: html, text
    Implement modes squish and pack for net tracks
• src/hg/hgTracks/pslTrack.c
  • 1.32 lines changed: 16, context: html, text, full: html, text
    Added logic to support gisaid.
  • 1.31 lines changed: 10, context: html, text, full: html, text
    Added logic to support gisaid.
• src/hg/hgTracks/wigTrack.c
  • 1.91 lines changed: 10, context: html, text, full: html, text
    It appears that these changes were committed in January, then stepped on in February
• src/hg/hgc/hgc.c
  • 1.1555 lines changed: 6, context: html, text, full: html, text
    avoid pop all warn handles; just hacked around it
  • 1.1554 lines changed: 4, context: html, text, full: html, text
    Added method of doH1n1Gene().
  • 1.1553 lines changed: 453, context: html, text, full: html, text
    added support for chimera in H1N1 prototype; also some refactoring
  • 1.1552 lines changed: 12, context: html, text, full: html, text
    Added the hook for Mark to add protein structure display stuff for H1N1.
• src/hg/hgc/makefile
  • 1.61 lines changed: 1, context: html, text, full: html, text
    added support for chimera in H1N1 prototype; also some refactoring
  • 1.60 lines changed: 6, context: html, text, full: html, text
    removed bash-specific syntax
• src/hg/hgc/virusClick.c
  • 1.7 lines changed: 52, context: html, text, full: html, text
    get gisaid locations from hg.conf
  • 1.6 lines changed: 18, context: html, text, full: html, text
    highlight only specific sequence differences in gene seq display
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Minor update.
  • 1.4 lines changed: 59, context: html, text, full: html, text
    Added details page for h1n1Gene.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Added isolate (sample view) link.
  • 1.2 lines changed: 13, context: html, text, full: html, text
    extract protein ids for dynamic_highlight script
  • 1.1 lines changed: 523, context: html, text, full: html, text
    added support for chimera in H1N1 prototype; also some refactoring
• src/hg/hgc/virusClick.h
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Added doH1n1Gene().
  • 1.1 lines changed: 8, context: html, text, full: html, text
    added support for chimera in H1N1 prototype; also some refactoring
• src/hg/inc/hui.h
  • 1.131 lines changed: 1, context: html, text, full: html, text
    Fixup chainCfgUi to work properly on split table names
• src/hg/instinct/bioInt2/makeClusterFiles.c
  • 1.1 lines changed: 974, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/makefile
  • 1.12 lines changed: 8, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/pathwayNullDist.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.12 lines changed: 68, context: html, text, full: html, text
    Added gray snp segmented data
• src/hg/lib/cart.c
  • 1.110 lines changed: 9, context: html, text, full: html, text
    Added stderr logging (a la htmlVaWarn) to cartEarlyWarningHandler, so we get an informative message along with the stack dump.
• src/hg/lib/hui.c
  • 1.213 lines changed: 14, context: html, text, full: html, text
    Kate didn't like colons, count occupied rows and columns in matrix, composteViewControlNameFromTdb didn't support ClosestToHome.
  • 1.212 lines changed: 240, context: html, text, full: html, text
    Huge Yale matrix requires right buttons and bottom buttons
  • 1.211 lines changed: 10, context: html, text, full: html, text
    Fixup chainCfgUi to work properly on split table names
  • 1.210 lines changed: 2, context: html, text, full: html, text
    Yale's many subtracks outgrew the 8 bit counter that I was using
  • 1.209 lines changed: 3, context: html, text, full: html, text
    Missing Restricted Until link
• src/hg/lib/jsHelper.c
  • 1.26 lines changed: 2, context: html, text, full: html, text
    I removed js file versioning by fake get variable, as it has led to some browsers/configurations reacquiring the file from the server every time a function is called. Versioning solution still remains to be done.
• src/hg/lib/web.c
  • 1.168 lines changed: 1, context: html, text, full: html, text
    Changed "subject view" to "sample view" for gisaid.
  • 1.167 lines changed: 38, context: html, text, full: html, text
    Added top bar section for GISAID.
• src/hg/makeDb/doc/aplCal1.txt
  • 1.9 lines changed: 4, context: html, text, full: html, text
    chains to sea hare
• src/hg/makeDb/doc/hg18.txt
  • 1.365 lines changed: 79, context: html, text, full: html, text
    Updated the wgRna track with latest miRBase and snoRNABase data.
• src/hg/makeDb/doc/hg19.txt
  • 1.25 lines changed: 92, context: html, text, full: html, text
    chains to sea hare
• src/hg/makeDb/doc/mm9.txt
  • 1.99 lines changed: 2, context: html, text, full: html, text
    Added a note to the miRNA track update section.
  • 1.98 lines changed: 5, context: html, text, full: html, text
    Fixed an off by 1 error in the BED file loaded for miRNA track.
  • 1.97 lines changed: 5, context: html, text, full: html, text
    Minor edits and added release date for miRNA data.
  • 1.96 lines changed: 4, context: html, text, full: html, text
    Re-loaded the miRNA track after adding scores that correspond to whether the sequence is on the + or - strand.
  • 1.95 lines changed: 47, context: html, text, full: html, text
    Updated the miRNA track to miRBase data release 13.0.
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.78 lines changed: 11, context: html, text, full: html, text
    Added gray breast cell line SNP6 segmented data
• src/hg/makeDb/trackDb/README
  • 1.77 lines changed: 14, context: html, text, full: html, text
    Added section describing settings specific to the snp125 (or later) tracks -- Kate's review feedback.
• src/hg/makeDb/trackDb/chainPanTro2.html
  • 1.3 lines changed: 7, context: html, text, full: html, text
    changed reference to fit pubmed model
• src/hg/makeDb/trackDb/human/cytoBand.html
  • 1.12 lines changed: 4, context: html, text, full: html, text
    changed reference to fit pubmed model
  • 1.11 lines changed: 26, context: html, text, full: html, text
    changed reference to fit pubmed model
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.396 lines changed: 19, context: html, text, full: html, text
    Removed wgRna track entry as duplicated from trackDb.ra at human level.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.351 lines changed: 81, context: html, text, full: html, text
    Added Yale/UCD K562b E2F6 and Setdb1
  • 1.350 lines changed: 30, context: html, text, full: html, text
    Consistency edits to Affy RNA. Need to get this into validator/loader
  • 1.349 lines changed: 22, context: html, text, full: html, text
    added new block for ENCODE Riken CAGE with release beta to get rid of non-pushed prostate cell line
  • 1.348 lines changed: 1, context: html, text, full: html, text
    Fixed metadata associated with moving excluded regions from open chramatin to mapability
  • 1.347 lines changed: 31, context: html, text, full: html, text
    Moved Excluded Regions to the Mapability track
  • 1.346 lines changed: 247, context: html, text, full: html, text
    Yale is one massive 2D array
  • 1.345 lines changed: 231, context: html, text, full: html, text
    More Yale Tables K562b/E2F2 and HepG2b/TR4
  • 1.344 lines changed: 1, context: html, text, full: html, text
    Typo on of of the billion tablenames
  • 1.343 lines changed: 288, context: html, text, full: html, text
    Added new Yale treatments, split out 'b' versions of K562 and HepG2, reworked some metadata
  • 1.342 lines changed: 8, context: html, text, full: html, text
    wgEncodeGencode names are not specific enough to warrant semiShortCircuit -- that was excluding UCSC Genes and other matches.
  • 1.341 lines changed: 3393, context: html, text, full: html, text
    Added a bunch of Yale treatments which necessitated breaking the composite between alpha nad beta and creating a 3D matrix for on alpha
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Minor wording change
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Moved Excluded Regions to the Mapability track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • 1.1 lines changed: 54, context: html, text, full: html, text
    Description for ENCODE variation track from HudsonAlpha
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Changed the wording for Duke excludable regions
  • 1.7 lines changed: 11, context: html, text, full: html, text
    Moved Excluded Regions to the Mapability track
  • 1.6 lines changed: 12, context: html, text, full: html, text
    Bryan updated his uniqueness methods
• src/hg/makeDb/trackDb/human/hg18/wgRnaJun09.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Removed reference to Blat.
  • 1.1 lines changed: 97, context: html, text, full: html, text
    Track description for the sno/miRNA track update.
• src/hg/makeDb/trackDb/human/hg19/hg18cytoBand.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    added comment about viewing mode
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Capitalized sentences
  • 1.1 lines changed: 10, context: html, text, full: html, text
    moved hg18ctoBand down to hg19 level and added html page for it
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
  • 1.1 lines changed: 155, context: html, text, full: html, text
    Adding a generic chain net description page for all the chains and nets
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Adding a generic chain net description page for all the chains and nets
  • 1.28 lines changed: 130, context: html, text, full: html, text
    Organizing the big chain net composites into clades
  • 1.27 lines changed: 46, context: html, text, full: html, text
    added blocks for chimp chain/nets to exist on beta and RR while composites are worked out on dev. removed some override stuff that was in there
  • 1.26 lines changed: 9, context: html, text, full: html, text
    moved hg18ctoBand down to hg19 level and added html page for it
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.463 lines changed: 1, context: html, text, full: html, text
    Changed long label of old wgRna track.
  • 1.462 lines changed: 2, context: html, text, full: html, text
    Updated short labels on sno/miRNA tracks.
  • 1.461 lines changed: 28, context: html, text, full: html, text
    After updating the wgRna track, renamed the old track to wgOld to keep it around for a while before replacing it with the new track.
  • 1.460 lines changed: 1, context: html, text, full: html, text
    Added html encoding for correct rendering of URL label for wgRna track.
  • 1.459 lines changed: 8, context: html, text, full: html, text
    moved hg18ctoBand down to hg19 level and added html page for it
  • 1.458 lines changed: 8, context: html, text, full: html, text
    enabled hg18ctyoBand track for comparison
• src/hg/makeDb/trackDb/human/wgRna.html
  • 1.7 lines changed: 55, context: html, text, full: html, text
    Updated description for updated wgRna track.
  • 1.6 lines changed: 11, context: html, text, full: html, text
    Updated wgRNA track description. hg18 is the only human assembly with the track at the moment.
• src/hg/makeDb/trackDb/human/wgRnaOld.html
  • 1.1 lines changed: 93, context: html, text, full: html, text
    wgRna track was updated to temporarily renamed old track to keep it around for a while before being replaced by the new track.
• src/hg/makeDb/trackDb/makefile
  • 1.269 lines changed: 1, context: html, text, full: html, text
    Added sacCer2 (why was it missing?).
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
  • 1.4 lines changed: 31, context: html, text, full: html, text
    Updated the miRNA track description after updating to Release 13.0 from miRBase. Added another reference.
• src/hg/makeDb/trackDb/mouse/mm9/miRNAMay2008.html
  • 1.1 lines changed: 80, context: html, text, full: html, text
    Old version of miRNA track description, use for release beta until new miRNA track released.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.49 lines changed: 1, context: html, text, full: html, text
    removed html extension for html line for miRNA release beta.
  • 1.48 lines changed: 15, context: html, text, full: html, text
    Added release alpha and beta versions of miRNA track until the update is released.
  • 1.47 lines changed: 1, context: html, text, full: html, text
    Re-enabled use of scoring for miRNA track.
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Added version number for update of miRNA track and removed useScore as there is no score for this track.
• src/hg/makeDb/trackDb/netPanTro2.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    changed reference to fit pubmed model
• src/hg/makeDb/trackDb/opossum/monDom5/gap.html
  • 1.2 lines changed: 54, context: html, text, full: html, text
    Reverted gold.html to top-level. Used gap.html form monDom4.
• src/hg/makeDb/trackDb/opossum/monDom5/gold.html
  • 1.3 lines changed: 26, context: html, text, full: html, text
    Reverted gold.html to top-level. Used gap.html form monDom4.
• src/hg/makeDb/trackDb/sacCer/sacCer2/sgdOther.html
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Fixup sgdOther reference to new assembly and turn off the score filter
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fixup sgdOther reference to new assembly and turn off the score filter
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.511 lines changed: 37, context: html, text, full: html, text
    Adding poodle chain/net
• src/hg/makeDb/trackDb/worm/priPac1/ctgPos2.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/priPac1/description.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/priPac1/gap.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/priPac1/gold.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makefile
  • 1.151 lines changed: 6, context: html, text, full: html, text
    only build encodeValidate on hgwdev/hgwbeta
• src/hg/ratStuff/mafSplitPos/mafSplitPos.c
  • 1.6 lines changed: 39, context: html, text, full: html, text
    This didn't work when gap and rmsk were not split tables, fix that up with more extensive MySQL queries
• src/lib/bigBed.c
  • 1.19 lines changed: 3, context: html, text, full: html, text
    don't bogusly crash on array or list colomns
• src/utils/bigBedSummary/bigBedSummary.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed non-portable code
• src/utils/bigWigSummary/bigWigSummary.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixed non-portable code
• src/utils/qa/commTrio.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed the hashpling so that this is run with tcsh.
• src/utils/qa/countPerChrom.csh
  • 1.13 lines changed: 1, context: html, text, full: html, text
    balanced a quote in a comment
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.63 lines changed: 2, context: html, text, full: html, text
    v209 preview

• lines changed: 8503
• files changed: 67