CVS changes by file

review to branch (2009-08-10 to 2009-08-18) v213

• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.40 lines changed: 17, context: html, text, full: html, text
    Added --generefs option to scan Google Scholar for references to genes by name
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Added --generefs option to scan Google Scholar for references to genes by name
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.45 lines changed: 3, context: html, text, full: html, text
    Added --generefs option to scan Google Scholar for references to genes by name
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.125 lines changed: 7, context: html, text, full: html, text
    Included the protocols
  • 1.124 lines changed: 23, context: html, text, full: html, text
    Four for Myers, two for Stam
  • 1.123 lines changed: 14, context: html, text, full: html, text
    Two protocols approved for Bernstein
  • 1.122 lines changed: 3, context: html, text, full: html, text
    Correct antibody name, by request of Rick Myers
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.44 lines changed: 41, context: html, text, full: html, text
    Consolidated a few statements, cleaned up a little bit.
  • 1.43 lines changed: 18, context: html, text, full: html, text
    Reformated a printf statement and removed a debugging function.
• src/hg/hgTables/bigWig.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/hgTables/filterFields.c
  • 1.79 lines changed: 6, context: html, text, full: html, text
    Don't enforce double- or int-checking on numeric sql fields because the filter inputs can be ranges too.
• src/hg/hgTracks/chainTrack.c
  • 1.35 lines changed: 6, context: html, text, full: html, text
    simplify computer chain normalized score gray scale suggest by jk
  • 1.34 lines changed: 4, context: html, text, full: html, text
    don't allow chain item to g white with normalize score
• src/hg/hgTracks/hgTracks.c
  • 1.1589 lines changed: 51, context: html, text, full: html, text
    Added support for new trackDb setting maxWindowToDraw: if winEnd-winStart>maxWindowToDraw, don't load or draw items, just print out a message telling the user how close they must zoom in to see items.
  • 1.1588 lines changed: 1, context: html, text, full: html, text
    Changes to reflect library changes dealing with the next-item button custom track bug. hGetBedRange wasn't up to the task.
  • 1.1587 lines changed: 2, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/hgTracks/simpleTracks.c
  • 1.96 lines changed: 7, context: html, text, full: html, text
    Changes to reflect library changes dealing with the next-item button custom track bug. hGetBedRange wasn't up to the task.
• src/hg/hgc/bigBedClick.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/hgc/rnaFoldClick.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fixed misuse of AllocVar macro detected by gcc 4.5
• src/hg/hgc/wiggleClick.c
  • 1.32 lines changed: 1, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/inc/bamFile.h
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixing 32-bit compatibility
• src/hg/inc/hdb.h
  • 1.168 lines changed: 6, context: html, text, full: html, text
    Change to hGetBedRange() for custom tracks. The problem was that hParseTableName expected a database to be passed to it that included a chromInfo table. customTrash isn't one of those databases, so instead we're also including the name of the database being browsed.
• src/hg/inc/versionInfo.h
  • 1.153 lines changed: 1, context: html, text, full: html, text
    "New version number v213"
• src/hg/instinct/bioInt2/bioPathwayLevel.c
  • 1.3 lines changed: 154, context: html, text, full: html, text
    Updated pipeline to be compatible with new binary
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.6 lines changed: 356, context: html, text, full: html, text
    Updated clinical features.
  • 1.5 lines changed: 226, context: html, text, full: html, text
    make the feature name readable.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.13 lines changed: 20, context: html, text, full: html, text
    added TCGA ovarian rna seq track
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fixed problem with unc g4502A
  • 1.11 lines changed: 83, context: html, text, full: html, text
    updated ovarian datasets
• src/hg/js/ajax.js
  • 1.5 lines changed: 9, context: html, text, full: html, text
    move getHgsid code to utils.js
• src/hg/js/cpJsFiles.pl
  • 1.3 lines changed: 15, context: html, text, full: html, text
    always get modification time right
• src/hg/js/hgTracks.js
  • 1.33 lines changed: 239, context: html, text, full: html, text
    back out inadvertent checkin of code
  • 1.32 lines changed: 239, context: html, text, full: html, text
    move getHgsid code to utils.js
• src/hg/js/jquery.contextmenu.js
  • 1.2 lines changed: 1, context: html, text, full: html, text
    pass event object to beforeShow callback
  • 1.1 lines changed: 264, context: html, text, full: html, text
    Version 1.0 downloaded from: http://www.javascripttoolbox.com/libsource.php/contextmenu/source/jquery.contextmenu.js
• src/hg/js/jquery.js
  • 1.2 lines changed: 16, context: html, text, full: html, text
    move getHgsid code to utils.js
• src/hg/js/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    fix typo of previous checkin (change to use cpJsFiles.pl)
  • 1.10 lines changed: 2, context: html, text, full: html, text
    move getHgsid code to utils.js
• src/hg/js/utils.js
  • 1.22 lines changed: 14, context: html, text, full: html, text
    add getHgsid
• src/hg/lib/altGraphX.c
  • 1.37 lines changed: 5, context: html, text, full: html, text
    fixed misuse of AllocVar macro detected by gcc 4.5
• src/hg/lib/customFactory.c
  • 1.100 lines changed: 22, context: html, text, full: html, text
    temporary workaround to help the keep-alive during transition to new variable name bigDataUrl
  • 1.99 lines changed: 31, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/lib/geneGraph.c
  • 1.25 lines changed: 3, context: html, text, full: html, text
    fixed misuse of AllocVar macro detected by gcc 4.5
• src/hg/lib/hdb.c
  • 1.409 lines changed: 14, context: html, text, full: html, text
    Change to hGetBedRange() for custom tracks. The problem was that hParseTableName expected a database to be passed to it that included a chromInfo table. customTrash isn't one of those databases, so instead we're also including the name of the database being browsed.
  • 1.408 lines changed: 3, context: html, text, full: html, text
    escape database name in hDbExists to fix error reported by sysadmin at NIH
• src/hg/lib/hui.c
  • 1.230 lines changed: 11, context: html, text, full: html, text
    Oops. Last change was tested 1/2 on the wrong browser. This ci is properly tested.
  • 1.229 lines changed: 11, context: html, text, full: html, text
    Multi-view settings should not show up in the table browser 'merge' function.
  • 1.228 lines changed: 3, context: html, text, full: html, text
    Fixed dimension Z to dynamically wrap when dimension X is dynamically reduced.
• src/hg/lib/jsHelper.c
  • 1.30 lines changed: 26, context: html, text, full: html, text
    restore dynamic creation of javascript symlinks which I deleted in version 1.29; rationale: to handle mirrors who don't preserve mtime's when rsync'ing
  • 1.29 lines changed: 22, context: html, text, full: html, text
    remove code in jsIncludeFile which dynamically creates the versioned softlinks (they have to be created via make install)
• src/hg/lib/ucscRetroCds.sql
  • 1.1 lines changed: 6, context: html, text, full: html, text
    initial version
• src/hg/makeDb/doc/hg17.txt
  • 1.122 lines changed: 19, context: html, text, full: html, text
    DGV updated to v8; changed color scheme to match their browser's.
• src/hg/makeDb/doc/hg18.txt
  • 1.376 lines changed: 22, context: html, text, full: html, text
    DGV updated to v8; changed color scheme to match their browser's.
• src/hg/makeDb/doc/hg19.txt
  • 1.35 lines changed: 212, context: html, text, full: html, text
    done with hg19 tetNig2 chain and net
• src/hg/makeDb/doc/oryCun2.txt
  • 1.1 lines changed: 167, context: html, text, full: html, text
    Initial browser built, running repeat masker and simple repeats
• src/hg/makeDb/doc/tetNig2.txt
  • 1.5 lines changed: 181, context: html, text, full: html, text
    done with hg19 tetNig2 chain and net
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.99 lines changed: 1, context: html, text, full: html, text
    Added tetNig2 - Tetraodon Nigirividis
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.347 lines changed: 8, context: html, text, full: html, text
    Adding automatic upstream file creation for ornAna1, fr2, gasAcu1, oryLat2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.104 lines changed: 1, context: html, text, full: html, text
    Added tetNig2 - Tetraodon Nigirividis
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.81 lines changed: 10, context: html, text, full: html, text
    added tcga ovarian RNA seq track
  • 1.80 lines changed: 78, context: html, text, full: html, text
    updated tcga ovarian cancer datasets
• src/hg/makeDb/schema/all.joiner
  • 1.731 lines changed: 6, context: html, text, full: html, text
    Adding tetNig2 and oryCun2
• src/hg/makeDb/trackDb/README
  • 1.87 lines changed: 1, context: html, text, full: html, text
    Added new setting maxWindowToDraw.
  • 1.86 lines changed: 10, context: html, text, full: html, text
    Adding docs on bigBed/bigWig types.
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to ganegoodall.org.
• src/hg/makeDb/trackDb/human/dgv.html
  • 1.4 lines changed: 8, context: html, text, full: html, text
    DGV updated to v8.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.490 lines changed: 30, context: html, text, full: html, text
    Correct TAF1 antibody name, by request of Rick Myers
  • 1.489 lines changed: 49, context: html, text, full: html, text
    Usability and consistency changes to UW Affy Exon track
  • 1.488 lines changed: 4, context: html, text, full: html, text
    some HA CNV changes
  • 1.487 lines changed: 29, context: html, text, full: html, text
    Changes to Caltech configuration and labels for clarity and consistency
  • 1.486 lines changed: 69, context: html, text, full: html, text
    Adjust display configuration based on input from Ali Mortazavi
  • 1.485 lines changed: 6, context: html, text, full: html, text
    more HA CNV fixes
  • 1.484 lines changed: 13, context: html, text, full: html, text
    change some colors and table names for HA CNV track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.11 lines changed: 27, context: html, text, full: html, text
    Add contacts, and minor corrections
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Link out
  • 1.4 lines changed: 36, context: html, text, full: html, text
    Cleanup for consistency
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.469 lines changed: 1, context: html, text, full: html, text
    added release alpha line to wgRnaOld track because it will not be going past dev
  • 1.468 lines changed: 1, context: html, text, full: html, text
    DGV updated to v8.
• src/hg/makeDb/trackDb/human/ucscRetroAli3.html
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Updated link and citation for an article.
• src/hg/makeDb/trackDb/makefile
  • 1.275 lines changed: 1, context: html, text, full: html, text
    Adding oryCun2 to the build
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed broken link to WUSTL.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.525 lines changed: 6, context: html, text, full: html, text
    Added new setting maxWindowToDraw to snp1* tracks, so they don't bog down views that are zoomed out way past the point where item display is meaningful.
  • 1.524 lines changed: 39, context: html, text, full: html, text
    Adding tetNig2 chain and net composite
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.52 lines changed: 26, context: html, text, full: html, text
    Added entry for Retroposed Genes version 1. Added search for the track.
• src/hg/makeDb/trackDb/zebrafish/ucscRetroAli1.html
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Draft of details page for UCSC Retrogenes predicted by RetroFinder.
• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
  • 1.22 lines changed: 14, context: html, text, full: html, text
    changed assert condition that was too strict (start >=0) instead of start > 0. Fixed compiler warnings.
• src/hg/tcga/scripts/DataTypes.py
  • 1.6 lines changed: 113, context: html, text, full: html, text
    added other tcga datasets
• src/hg/tcga/scripts/GenericDataType.py
  • 1.6 lines changed: 57, context: html, text, full: html, text
    added other tcga datasets
• src/hg/tcga/scripts/processData.py
  • 1.9 lines changed: 49, context: html, text, full: html, text
    added other tcga datasets
• src/hg/txGraph/txgAddEvidence/txgAddEvidence.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    fixed misuse of AllocVar macro detected by gcc 4.5
• src/hg/utils/automation/blastz-run-ucsc
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Proper reference to /bin/ls instead of just ls in a system() call to avoid PATH searching
• src/hg/utils/automation/makefile
  • 1.14 lines changed: 4, context: html, text, full: html, text
    added make test, simplify rules
• src/hg/utils/makefile
  • 1.15 lines changed: 56, context: html, text, full: html, text
    added make test, simplify rules
  • 1.14 lines changed: 5, context: html, text, full: html, text
    added initial implementation of gff3ToGenePred converter
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.7 lines changed: 3, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSledgeHammer.pl
  • 1.4 lines changed: 4, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl
• src/inc/asParse.h
  • 1.6 lines changed: 12, context: html, text, full: html, text
    add some memory clean up routines
• src/inc/bbiFile.h
  • 1.14 lines changed: 7, context: html, text, full: html, text
    add some memory clean up routines
  • 1.13 lines changed: 7, context: html, text, full: html, text
    Moving some functions from bedGraphToBigBed to library.
• src/inc/gff3.h
  • 1.2 lines changed: 53, context: html, text, full: html, text
    added initial implementation of gff3ToGenePred converter
• src/inc/options.h
  • 1.14 lines changed: 3, context: html, text, full: html, text
    add some memory clean up routines
• src/lib/asParse.c
  • 1.9 lines changed: 55, context: html, text, full: html, text
    add some memory clean up routines
• src/lib/bbiRead.c
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Fixing bug in coverage calcs.
• src/lib/bbiWrite.c
  • 1.5 lines changed: 27, context: html, text, full: html, text
    add some memory clean up routines
  • 1.4 lines changed: 72, context: html, text, full: html, text
    Moving some functions from bedGraphToBigBed to library.
• src/lib/bigBed.c
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Moving some functions from bedGraphToBigBed to library.
• src/lib/errCatch.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix using variable string where a format should be, detected by gcc 4.3.3
• src/lib/gff3.c
  • 1.3 lines changed: 33, context: html, text, full: html, text
    added initial implementation of gff3ToGenePred converter
• src/lib/htmshell.c
  • 1.62 lines changed: 1, context: html, text, full: html, text
    remove now unneeded code - thanks Brian for the review
• src/lib/options.c
  • 1.26 lines changed: 6, context: html, text, full: html, text
    add some memory clean up routines
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Bumping up default itemsPerSlot for better efficiency.
• src/utils/bigBedToBed/bigBedToBed.c
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Making it handle 3 column beds better.
• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removing unused include file.
• src/utils/qa/qaEnsGenes.csh
  • 1.23 lines changed: 1, context: html, text, full: html, text
    adding sort to a sql query so it's easier to find your db
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.72 lines changed: 3, context: html, text, full: html, text
    v213 final build
• src/utils/userApps/bigBedWigs.txt
  • 1.4 lines changed: 2, context: html, text, full: html, text
    handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl

• lines changed: 3757
• files changed: 84