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
- 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
- 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
- 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
- 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
- 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