CVS changes by file
review to branch (2010-02-10 to 2010-02-16) v225
- src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
- 1.11 lines changed: 579, context: html, text, full: html, text
recover code for JGI, string, and easygene tracks
- src/hg/archaeStuff/tooltip/tooltip.c
- 1.7 lines changed: 60, context: html, text, full: html, text
integrated archae tool tip changes from Andrew Holmes
- src/hg/blastToPsl/makefile
- 1.30 lines changed: 1, context: html, text, full: html, text
kent/src/lib is 2, not 3 directory levels above.
- src/hg/encode/encodeValidate/config/cv.ra
- 1.213 lines changed: 15, context: html, text, full: html, text
Temporarily commented out MCF-10A.
- 1.212 lines changed: 17, context: html, text, full: html, text
Added the MCF-10A cll type
- src/hg/hgGateway/hgGateway.c
- 1.114 lines changed: 23, context: html, text, full: html, text
add gene autosuggest field
- src/hg/hgGetAnn/hgGetAnn.c
- 1.7 lines changed: 2, context: html, text, full: html, text
Added cgiSpoof so the new cgiOptionalString in hgFind.c doesn't make cgiInit freak out.
- src/hg/hgTracks/bamTrack.c
- 1.25 lines changed: 5, context: html, text, full: html, text
Fix: handle soft-clipping when fetching query sequence.
- src/hg/hgTracks/hgTracks.c
- 1.1628 lines changed: 2, context: html, text, full: html, text
move ajax.js include into dragZooming block
- 1.1627 lines changed: 10, context: html, text, full: html, text
add gene autosuggestion
- 1.1626 lines changed: 10, context: html, text, full: html, text
One more minor adjustment to navagation links
- 1.1625 lines changed: 57, context: html, text, full: html, text
This work allows separate image fro sideLabels which is necessary for dragScroll off end of an image.
- 1.1624 lines changed: 23, context: html, text, full: html, text
Removed ifdef IMAGE_V2. This is now permenant. Also rearranged optional navigation links
- src/hg/hgTracks/imageV2.c
- 1.24 lines changed: 10, context: html, text, full: html, text
This work allows separate image fro sideLabels which is necessary for dragScroll off end of an image.
- 1.23 lines changed: 66, context: html, text, full: html, text
Removed ifdef IMAGE_V2. Work to move style to common classes. Work for dragScroll.
- src/hg/hgTracks/imageV2.h
- 1.16 lines changed: 16, context: html, text, full: html, text
This work allows separate image fro sideLabels which is necessary for dragScroll off end of an image.
- 1.15 lines changed: 25, context: html, text, full: html, text
Removed ifdef IMAGE_V2. This is now permenant. Also worked on dragScroll size 1x.
- src/hg/hgc/bamClick.c
- 1.16 lines changed: 1, context: html, text, full: html, text
Added printTrackUiLink in doBamDetails.
- 1.15 lines changed: 8, context: html, text, full: html, text
Fix: handle soft-clipping when fetching query sequence.
- src/hg/hgc/hgc.h
- 1.49 lines changed: 3, context: html, text, full: html, text
Added printTrackUiLink in doBamDetails.
- src/hg/inc/bamFile.h
- 1.14 lines changed: 6, context: html, text, full: html, text
Fix: handle soft-clipping when fetching query sequence.
- src/hg/inc/versionInfo.h
- 1.166 lines changed: 1, context: html, text, full: html, text
"New version number v225"
- src/hg/instinct/hgGeneset/frontend/css/hgHeatmapStyle.css
- 1.7 lines changed: 32, context: html, text, full: html, text
Got features kinda working
- src/hg/instinct/hgGeneset/frontend/genesetView.html
- 1.8 lines changed: 14, context: html, text, full: html, text
Got features kinda working
- src/hg/instinct/hgGeneset/frontend/js/hgHeatmapGeneset.js
- 1.10 lines changed: 95, context: html, text, full: html, text
Got features kinda working
- src/hg/instinct/hgGeneset/hgGenesets.c
- 1.15 lines changed: 12, context: html, text, full: html, text
update getmatching
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
- 1.14 lines changed: 314, context: html, text, full: html, text
Fixed OV Clinical Data
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
- 1.24 lines changed: 2, context: html, text, full: html, text
Fixed the patient db and rafile
- 1.23 lines changed: 22, context: html, text, full: html, text
Fixed the patient db and rafile
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.su2c.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
- 1.78 lines changed: 12, context: html, text, full: html, text
Changed feature sliders to support floating point
- src/hg/instinct/hgMicroscope/microscope/hgMicroscope.c
- src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch.o
- 1.2 lines changed: 0, context: html, text, full: html, text
.o files should not be checked in.
- src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/vgLoadTest.o
- 1.2 lines changed: 0, context: html, text, full: html, text
.o files should not be checked in.
- src/hg/instinct/hgMicroscope/microscopeLoad/test/test.ra
- src/hg/instinct/hgMicroscope/microscopeLoad/test/test.tab
- src/hg/instinct/hgMicroscope/microscopeLoad/test/testcaptions.txt
- src/hg/js/ajax.js
- 1.6 lines changed: 18, context: html, text, full: html, text
move some code here from hgTracks.js
- src/hg/js/autocomplete.js
- src/hg/js/hgTracks.js
- 1.54 lines changed: 111, context: html, text, full: html, text
add autocomplete code; add getDna support
- 1.53 lines changed: 7, context: html, text, full: html, text
This work allows separate image fro sideLabels which is necessary for dragScroll off end of an image.
- 1.52 lines changed: 94, context: html, text, full: html, text
Good work on dragScroll. Ajax refresh of whole image not yet working but form.submit() works.
- src/hg/js/lowetooltip.js
- 1.2 lines changed: 42, context: html, text, full: html, text
integrated archae tool tip changes from Andrew Holmes
- src/hg/js/makefile
- 1.14 lines changed: 2, context: html, text, full: html, text
add autocomplete files
- src/hg/js/utils.js
- 1.28 lines changed: 24, context: html, text, full: html, text
move some code here from hgTracks.js
- src/hg/lib/bamFile.c
- 1.19 lines changed: 38, context: html, text, full: html, text
Fix: handle soft-clipping when fetching query sequence.
- src/hg/lib/hgFind.c
- 1.225 lines changed: 4, context: html, text, full: html, text
In searchKnownCanonical, no need to include knownGene in the query because kgXref and knownCanonical can be joined directly - thanks for catching that Tim.
- src/hg/lib/hui.c
- 1.260 lines changed: 5, context: html, text, full: html, text
Fixed an onerouus bug in last ci that Angie and Brian both found.
- src/hg/lib/rgdGeneRaw0.sql
- 1.1 lines changed: 12, context: html, text, full: html, text
Created rgdGeneRaw0.sql, an interim table for rgdGene build.
- src/hg/lib/rgdGeneRaw2.sql
- 1.1 lines changed: 12, context: html, text, full: html, text
Created rgdGeneRaw2.sql, an interium table used for RGD Genes build.
- src/hg/lib/rgdGeneRaw3.sql
- 1.1 lines changed: 12, context: html, text, full: html, text
Created rgdGeneRaw3.sql, an interium table used for RGD Genes build.
- src/hg/makeDb/doc/ailMel1.txt
- 1.4 lines changed: 81, context: html, text, full: html, text
rebuild Panda sequence with official genbank release
- src/hg/makeDb/doc/aplCal1.txt
- 1.12 lines changed: 7, context: html, text, full: html, text
adding image for Aplysia
- src/hg/makeDb/doc/calJac1.txt
- 1.22 lines changed: 12, context: html, text, full: html, text
liftOver to calJac3 completed
- src/hg/makeDb/doc/calJac3.txt
- 1.3 lines changed: 378, context: html, text, full: html, text
done with a number of lastz runs
- 1.2 lines changed: 166, context: html, text, full: html, text
started Human proteins
- src/hg/makeDb/doc/canFam2.txt
- 1.28 lines changed: 15, context: html, text, full: html, text
completed calJac3 lastz alignment
- 1.27 lines changed: 59, context: html, text, full: html, text
rerun the panda alignment, and starting the calJac3 marmoset
- src/hg/makeDb/doc/hg19.txt
- 1.82 lines changed: 68, context: html, text, full: html, text
rerun the Panda lastz, and the calJac3
- src/hg/makeDb/doc/mm9.txt
- 1.125 lines changed: 48, context: html, text, full: html, text
completed calJac3 lastz alignment
- src/hg/makeDb/doc/monDom5.txt
- 1.19 lines changed: 48, context: html, text, full: html, text
completed calJac3 lastz alignment
- src/hg/makeDb/doc/oryCun2.txt
- 1.6 lines changed: 22, context: html, text, full: html, text
all.joiner done and pushQ entries
- src/hg/makeDb/doc/panTro2.txt
- 1.18 lines changed: 63, context: html, text, full: html, text
last runs to Marmoset calJac3
- src/hg/makeDb/doc/ponAbe2.txt
- 1.23 lines changed: 61, context: html, text, full: html, text
last runs to Marmoset calJac3
- src/hg/makeDb/doc/rheMac2.txt
- 1.20 lines changed: 61, context: html, text, full: html, text
last runs to Marmoset calJac3
- src/hg/makeDb/doc/rn4.txt
- 1.38 lines changed: 117, context: html, text, full: html, text
Added RGD Genes build pipeline.
- src/hg/makeDb/doc/tetNig2.txt
- 1.9 lines changed: 8, context: html, text, full: html, text
add cpgIslandExt track
- src/hg/makeDb/genbank/etc/align.dbs
- 1.111 lines changed: 1, context: html, text, full: html, text
Adding calJac3 - Marmoset - Callithrix jacchus
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- 1.115 lines changed: 1, context: html, text, full: html, text
Adding calJac3 - Marmoset - Callithrix jacchus
- src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
- src/hg/makeDb/trackDb/README
- 1.101 lines changed: 15, context: html, text, full: html, text
Replacing subTrack with parent
- src/hg/makeDb/trackDb/ancestor/trackDb.ra
- 1.11 lines changed: 4, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.10 lines changed: 4, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/cat/trackDb.ra
- 1.13 lines changed: 3, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.12 lines changed: 3, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/chicken/trackDb.ra
- 1.26 lines changed: 6, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/chimp/trackDb.ra
- 1.36 lines changed: 6, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/drosophila/dm1/trackDb.ra
- 1.62 lines changed: 3, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.61 lines changed: 3, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
- 1.62 lines changed: 29, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.61 lines changed: 29, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/drosophila/trackDb.ra
- 1.86 lines changed: 76, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.85 lines changed: 76, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/fugu/trackDb.ra
- 1.79 lines changed: 8, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/hiv/trackDb.ra
- 1.7 lines changed: 28, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.6 lines changed: 28, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/human/hg16/trackDb.ra
- 1.588 lines changed: 11, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.587 lines changed: 11, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/human/hg17/trackDb.ra
- 1.454 lines changed: 71, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.453 lines changed: 71, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- 1.468 lines changed: 195, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.467 lines changed: 195, context: html, text, full: html, text
Changing subTrack to parent.
- 1.466 lines changed: 24, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- 1.866 lines changed: 1500, context: html, text, full: html, text
extract CalTech RNA-seq to its own set of files
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
- 1.1 lines changed: 1537, context: html, text, full: html, text
extracting Caltech RNA-seq track to its own set of files
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.beta.ra
- 1.1 lines changed: 1535, context: html, text, full: html, text
extracting Caltech RNA-seq track to its own set of files
- src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
- 1.17 lines changed: 3, context: html, text, full: html, text
Minor edit.
- 1.16 lines changed: 1, context: html, text, full: html, text
Adding HTML encoding.
- 1.15 lines changed: 25, context: html, text, full: html, text
Updated CRG Mapability track description with text from data providers.
- src/hg/makeDb/trackDb/human/hg19/encMapability.html
- 1.2 lines changed: 1, context: html, text, full: html, text
Minor edit.
- 1.1 lines changed: 49, context: html, text, full: html, text
Description for Mapability track.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- 1.98 lines changed: 143, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.97 lines changed: 143, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/human/trackDb.ra
- 1.515 lines changed: 172, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.514 lines changed: 172, context: html, text, full: html, text
Changing subTrack to parent.
- 1.513 lines changed: 7, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/human/wgEncodeGencode.html
- 1.7 lines changed: 13, context: html, text, full: html, text
a few small typos, and shortening lines to 80
- src/hg/makeDb/trackDb/loadTracks
- 1.19 lines changed: 1, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
- 1.8 lines changed: 5, context: html, text, full: html, text
Add monDom5 for calJac3
- src/hg/makeDb/trackDb/medaka/trackDb.ra
- 1.28 lines changed: 6, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
- 1.66 lines changed: 2, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.65 lines changed: 2, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
- 1.67 lines changed: 49, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.66 lines changed: 49, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- 1.84 lines changed: 24, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.83 lines changed: 24, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/mouse/trackDb.ra
- 1.208 lines changed: 5, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.207 lines changed: 5, context: html, text, full: html, text
Changing subTrack to parent.
- 1.206 lines changed: 8, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/opossum/trackDb.ra
- 1.53 lines changed: 6, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.52 lines changed: 6, context: html, text, full: html, text
Changing subTrack to parent.
- 1.51 lines changed: 6, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/rat/trackDb.ra
- 1.80 lines changed: 2, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.79 lines changed: 2, context: html, text, full: html, text
Changing subTrack to parent.
- 1.78 lines changed: 6, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/sacCer/trackDb.ra
- 1.48 lines changed: 6, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.47 lines changed: 6, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/stickleback/trackDb.ra
- 1.33 lines changed: 9, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/tetraodon/trackDb.ra
- 1.59 lines changed: 8, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- 1.80 lines changed: 4, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/trackDb.ra
- 1.617 lines changed: 27, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
- 1.42 lines changed: 7, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.41 lines changed: 7, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
- 1.22 lines changed: 28, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.21 lines changed: 28, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/worm/trackDb.ra
- 1.42 lines changed: 20, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.41 lines changed: 20, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
- 1.27 lines changed: 19, context: html, text, full: html, text
moved all danRer4 chains and nets to composite and dropped individual tracks
- src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
- 1.34 lines changed: 4, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.33 lines changed: 4, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/makeDb/trackDb/zebrafish/trackDb.ra
- 1.73 lines changed: 4, context: html, text, full: html, text
Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up.
- 1.72 lines changed: 4, context: html, text, full: html, text
Changing subTrack to parent.
- src/hg/oneShot/tdbRewriteSubtrackToParent/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
Utility to replace subTrack with parent seems to work.
- src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
- 1.1 lines changed: 129, context: html, text, full: html, text
Utility to replace subTrack with parent seems to work.
- src/hg/utils/automation/doBlastzChainNet.pl
- 1.31 lines changed: 9, context: html, text, full: html, text
not loading split table is now the default
- src/hg/utils/automation/doCpgIslands.pl
- 1.3 lines changed: 7, context: html, text, full: html, text
check source input for enough valid bases before running cpglh.exe
- src/hg/utils/automation/doEnsGeneUpdate.pl
- 1.23 lines changed: 9, context: html, text, full: html, text
now adding dateReference to the trackVersion table entry
- src/hg/visiGene/microscope.as
- 1.2 lines changed: 60, context: html, text, full: html, text
Removing - Chris says they are not needed here.
- src/hg/visiGene/microscope.sql
- 1.2 lines changed: 88, context: html, text, full: html, text
Removing - Chris says they are not needed here.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/cvs-reports-d
- 1.16 lines changed: 8, context: html, text, full: html, text
removing BASE for now, caused problems with but ran without on review reports 2/11/2010
- src/utils/qa/weeklybld/cvs-reports-delta
- 1.10 lines changed: 1, context: html, text, full: html, text
keep more debugging info in output about commandline
- lines changed: 10250
- files changed: 109