CVS changes by file
branch to review (2009-09-02 to 2009-09-09) v214
- java/src/edu/ucsc/genome/qa/cgiCheck/full.props
- src/hg/archaeStuff/data/Genome-info-mods
- 1.77 lines changed: 2, context: html, text, full: html, text
fix contig names in N. magadii
- src/hg/archaeStuff/scripts/archaeBrowser/AlignmentCompare.pm
- 1.4 lines changed: 32, context: html, text, full: html, text
Altered for new conservation files
- 1.3 lines changed: 48, context: html, text, full: html, text
Fixed file opening failure
- src/hg/archaeStuff/scripts/archaeBrowser/ConservedDomains.pm
- src/hg/archaeStuff/scripts/archaeBrowser/GEOmicroarrays.pm
- src/hg/archaeStuff/scripts/archaeBrowser/SEED.pm
- src/hg/archaeStuff/scripts/archaeBrowser/tigr.pm
- src/hg/encode/DAFs/GisDnaPet.daf
- 1.4 lines changed: 2, context: html, text, full: html, text
add validateFiles command line
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- 1.70 lines changed: 1, context: html, text, full: html, text
ln to right place with bigBed files
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- 1.192 lines changed: 2, context: html, text, full: html, text
Protection from when no validationSettings have been provided
- 1.191 lines changed: 7, context: html, text, full: html, text
Removed hack to default missing RawSignal to on. This has the affect that raw signals are no longer auto-created unless the view is specifically defined in the DAF.
- 1.190 lines changed: 31, context: html, text, full: html, text
Expanded valitationSettings support to handle ignoreAlignment and ignoreChromLen
- src/hg/encode/validateFiles/makefile
- 1.3 lines changed: 1, context: html, text, full: html, text
Add to L instead of overwriting -- need common.mk's handling of USE_SSL.
- src/hg/geneBounds/motifLogo/motifLogo.c
- 1.7 lines changed: 36, context: html, text, full: html, text
added option to control minimum height of a sequence logo column
- src/hg/hgGetAnn/tests/expected/chrRangeGenePred.gp
- 1.3 lines changed: 2, context: html, text, full: html, text
Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
- src/hg/hgGetAnn/tests/expected/chrRangeGenePredColHeaders.gp
- 1.3 lines changed: 2, context: html, text, full: html, text
Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
- src/hg/hgGetAnn/tests/expected/chrRangeGenePredTsvHeaders.gp
- 1.3 lines changed: 2, context: html, text, full: html, text
Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order.
- src/hg/hgTrackUi/hgTrackUi.c
- 1.500 lines changed: 30, context: html, text, full: html, text
Basic ui for type bam -- still need to add filtering on BAM flag bits.
- src/hg/hgTracks/bamTrack.c
- 1.8 lines changed: 43, context: html, text, full: html, text
Added basic filtering on hgTrackUi settings. Make paired-but-not-properly items a lighter shade.
- src/hg/hgTracks/hgTracks.c
- 1.1596 lines changed: 9, context: html, text, full: html, text
Changes for imgTbl withot dragReorder or dragScroll
- src/hg/hgTracks/imageV2.c
- 1.9 lines changed: 35, context: html, text, full: html, text
Changes for imgTbl withot dragReorder or dragScroll
- src/hg/hgTracks/imageV2.h
- 1.6 lines changed: 10, context: html, text, full: html, text
Changes for imgTbl withot dragReorder or dragScroll
- src/hg/hgTracks/simpleTracks.c
- 1.100 lines changed: 1, context: html, text, full: html, text
Registered wgEncodeGencode composite to use gencodeGeneMethods
- src/hg/hgTracks/wigCommon.h
- 1.7 lines changed: 2, context: html, text, full: html, text
always include 0 logic
- src/hg/hgTracks/wigTrack.c
- 1.92 lines changed: 10, context: html, text, full: html, text
always include 0 logic
- src/hg/hgc/hgc.c
- 1.1571 lines changed: 16, context: html, text, full: html, text
integrated carefully reviewed changes from Robert to retro gene details page
- 1.1570 lines changed: 7, context: html, text, full: html, text
Changed code for Ensembl and Vega message given on details page if there is no protein prediction available.
- src/hg/hgc/lowelab.c
- 1.34 lines changed: 55, context: html, text, full: html, text
removing allpredictions.h
- 1.33 lines changed: 171, context: html, text, full: html, text
Predicted genes
- src/hg/hgc/retroClick.c
- 1.13 lines changed: 31, context: html, text, full: html, text
integrated carefully reviewed changes from Robert to retro gene details page
- src/hg/inc/alignInfo.h
- 1.1 lines changed: 71, context: html, text, full: html, text
Adding alignment info
- src/hg/inc/cddInfo.h
- 1.1 lines changed: 71, context: html, text, full: html, text
Adding coverage and percent positive
- src/hg/inc/hui.h
- src/hg/inc/wiggle.h
- src/hg/instinct/bioInt2/bioController.c
- 1.14 lines changed: 1, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioController.h
- 1.9 lines changed: 1, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioIntDb.c
- 1.9 lines changed: 61, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioIntDb.h
- 1.8 lines changed: 33, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioIntDriver.h
- 1.8 lines changed: 1, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioPathway.h
- 1.2 lines changed: 7, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioPathwayLevel.c
- 1.5 lines changed: 49, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
- 1.2 lines changed: 100, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/createTables.c
- 1.4 lines changed: 2, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/bioInt2/makeClusterFiles.c
- 1.3 lines changed: 5, context: html, text, full: html, text
Added em to pipeline
- src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl
- 1.1 lines changed: 127, context: html, text, full: html, text
perl code to generate description html files
- src/hg/instinct/createDescriptionHTML/generateAllDescriptionHTMLs.pl
- 1.1 lines changed: 81, context: html, text, full: html, text
perl code to generate description html files
- src/hg/instinct/createDescriptionHTML/makefile
- 1.1 lines changed: 13, context: html, text, full: html, text
perl code to generate description html files
- src/hg/instinct/createDescriptionHTML/removeAllDescriptionHTMLs.pl
- 1.1 lines changed: 3, context: html, text, full: html, text
perl code to generate description html files
- src/hg/instinct/hgHeatmap2/hgAnnotations.c
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb.instinct.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_basso2005.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenGBMBio.ra
- 1.4 lines changed: 17, context: html, text, full: html, text
modify columnDB for GBM controlled data
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinGBMBio.ra
- 1.2 lines changed: 0, context: html, text, full: html, text
modify dataset.TCGAopen.ra and dataset.TCGAcontrol.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_vijver2002.ra
- 1.3 lines changed: 1, context: html, text, full: html, text
fixed bug with non-escaped chars
- 1.2 lines changed: 1, context: html, text, full: html, text
removed single quote
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
- 1.17 lines changed: 185, context: html, text, full: html, text
modify dataset.TCGAopen.ra and dataset.TCGAcontrol.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAopen.ra
- 1.6 lines changed: 40, context: html, text, full: html, text
- 1.5 lines changed: 316, context: html, text, full: html, text
modify dataset.TCGAopen.ra and dataset.TCGAcontrol.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
- 1.20 lines changed: 30, context: html, text, full: html, text
added some wrangling stuff
- 1.19 lines changed: 229, context: html, text, full: html, text
Updated with new descriptor fields
- 1.18 lines changed: 9, context: html, text, full: html, text
Fields for data descriptions shown in Mullighan2008_SNP6 entry. Fill yours in!
- 1.17 lines changed: 1, context: html, text, full: html, text
modify dataset.TCGAopen.ra and dataset.TCGAcontrol.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/hgHeatmapStyle.css
- 1.18 lines changed: 3, context: html, text, full: html, text
fix layout bugs
- 1.17 lines changed: 1, context: html, text, full: html, text
tooltip window resizing
- src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
- 1.35 lines changed: 2, context: html, text, full: html, text
removed links to old help page
- src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/pathway.html
- 1.2 lines changed: 1, context: html, text, full: html, text
removed links to old help page
- src/hg/instinct/hgHeatmap2/hgSessions.c
- 1.8 lines changed: 3, context: html, text, full: html, text
fixed bug with non-escaped chars
- src/hg/instinct/webUserAdmin/webUserAdmin.c
- 1.10 lines changed: 2, context: html, text, full: html, text
Connect to membership DB in localDb.
- src/hg/js/hui.js
- 1.32 lines changed: 30, context: html, text, full: html, text
Cleaned up more non-jquery syntax and made multi-selects work with subtrack cfg updating
- 1.31 lines changed: 20, context: html, text, full: html, text
Fix for crazy quantum entanglement bug that Brooke found on cons 44-way
- src/hg/lib/alignInfo.as
- 1.1 lines changed: 15, context: html, text, full: html, text
adding aligned features autosql
- src/hg/lib/alignInfo.c
- 1.1 lines changed: 177, context: html, text, full: html, text
Adding alignment info
- src/hg/lib/cddInfo.as
- src/hg/lib/cddInfo.c
- 1.1 lines changed: 177, context: html, text, full: html, text
Adding coverage and percent positive
- src/hg/lib/cddInfo.sql
- 1.1 lines changed: 21, context: html, text, full: html, text
Adding coverage and percent positive
- src/hg/lib/hdb.c
- 1.414 lines changed: 18, context: html, text, full: html, text
backed out change to use hTableExists in some places, as it attempts to access the cache while it's being build in certain cases
- src/hg/lib/hui.c
- 1.236 lines changed: 28, context: html, text, full: html, text
Fixed configurable subtracks to not depend upon subgroup/view membership
- 1.235 lines changed: 19, context: html, text, full: html, text
always include 0 option
- 1.234 lines changed: 3, context: html, text, full: html, text
wgEncodeSangerGencode for Rel2 but wgEncodeGencode for V3
- src/hg/lib/makefile
- 1.394 lines changed: 2, context: html, text, full: html, text
Adding alignment and domain tracks
- src/hg/lib/trackDbCustom.c
- 1.70 lines changed: 2, context: html, text, full: html, text
Added bam to packableType().
- src/hg/lib/wiggleCart.c
- 1.21 lines changed: 21, context: html, text, full: html, text
always include 0 option
- src/hg/lib/wiggleUtils.c
- 1.55 lines changed: 3, context: html, text, full: html, text
if there's no wiggle on a chrom, just assume minSpan is 1 since we won't end up using this value anyway. TIME TO GET RID OF THESE WIGGLES!!
- src/hg/logCrawl/accessLogSort/accessLogSort.c
- 1.1 lines changed: 73, context: html, text, full: html, text
Sorter for access logs, currently just by timestamp.
- src/hg/logCrawl/accessLogSort/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
Sorter for access logs, currently just by timestamp.
- src/hg/logCrawl/accessLogWigs/accessLogWigs.c
- 1.2 lines changed: 3, context: html, text, full: html, text
Removing some debugging code.
- src/hg/logCrawl/crawlForHogs/crawlForHogs.c
- 1.3 lines changed: 29, context: html, text, full: html, text
Adding a few more troughs to the hog-finder.
- src/hg/logCrawl/crawlForPosAndTime/crawlForPosAndTime.c
- 1.1 lines changed: 97, context: html, text, full: html, text
Utility to yank out window size and some timing info on logs seems to work.
- src/hg/logCrawl/crawlForPosAndTime/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
Utility to yank out window size and some timing info on logs seems to work.
- src/hg/logCrawl/ticksToWig/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
Utility to convert tab-separated files with Unix timestamps and optionally a number to wiggle plots seems to work.
- src/hg/logCrawl/ticksToWig/ticksToWig.c
- 1.1 lines changed: 129, context: html, text, full: html, text
Utility to convert tab-separated files with Unix timestamps and optionally a number to wiggle plots seems to work.
- src/hg/makeDb/doc/canFam2.txt
- 1.24 lines changed: 8, context: html, text, full: html, text
Small note about creating monDom5 chains/nets (swapped) on canFam2.
- 1.23 lines changed: 11, context: html, text, full: html, text
Unsplit tables for monDom5 chains on canFam2.
- src/hg/makeDb/doc/hg18.txt
- 1.381 lines changed: 47, context: html, text, full: html, text
Documented code changes and reloaded vegaPep table with only those proteins whose transcripts are in vegaGtp.
- 1.380 lines changed: 16, context: html, text, full: html, text
Documented reloading tables after reversion to older data during mySQL upgrade.
- 1.379 lines changed: 20, context: html, text, full: html, text
Added a vegaPep table for the Vega Genes update.
- src/hg/makeDb/doc/hg19.txt
- 1.37 lines changed: 54, context: html, text, full: html, text
Added snp130CodingDbSnp (used dbSNP's provisional SNP coord mapping from hg18).
- src/hg/makeDb/doc/mm9.txt
- 1.111 lines changed: 33, context: html, text, full: html, text
Added NIA Gene Index.
- 1.110 lines changed: 46, context: html, text, full: html, text
Documented code changes and reloaded vegaPep table with only those proteins whose transcripts are in vegaGtp.
- 1.109 lines changed: 19, context: html, text, full: html, text
Documented creation of vega35 directory. Documented reloading tables after some of them reverted to older versions during mySQL upgrade.
- 1.108 lines changed: 23, context: html, text, full: html, text
Added a vegaPep table for the Vega Genes update.
- src/hg/makeDb/genbank/etc/genbank.conf
- 1.348 lines changed: 1, context: html, text, full: html, text
enabled ccds on hg19
- src/hg/makeDb/schema/all.joiner
- 1.734 lines changed: 2, context: html, text, full: html, text
adding new table: vegaPep
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- 1.416 lines changed: 1, context: html, text, full: html, text
Changed colour for vega genes to distinguish them more clearly from the pseudogenes subtrack.
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- 1.514 lines changed: 39, context: html, text, full: html, text
A bunch of color changes for Gencode.
- 1.513 lines changed: 2, context: html, text, full: html, text
get the right kind of bed in there
- 1.512 lines changed: 65, context: html, text, full: html, text
Splitting out RNA-seq PolyA tails into separate composte in Expression group
- 1.511 lines changed: 81, context: html, text, full: html, text
Added K562b/GATA-2 and K562b/YY1 for Yale/UCDavis
- 1.510 lines changed: 9, context: html, text, full: html, text
Cleaned up metadata for wgEncode Gencode
- 1.509 lines changed: 38, context: html, text, full: html, text
Added wgEncodeGencode search specs and fixed some longLabels
- 1.508 lines changed: 92, context: html, text, full: html, text
wgEncodeGencode V3 (alpha) and wgEcodeSangerGencode Rel2 (beta)
- 1.507 lines changed: 26, context: html, text, full: html, text
wgEncodeGisRnaSeqAlignmentsK562Cytosol
- 1.506 lines changed: 1, context: html, text, full: html, text
fixed bug where replicate 2 was labeled as replicate 1
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
- 1.11 lines changed: 1, context: html, text, full: html, text
Made the link to the myers lab open in a new window
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
- 1.36 lines changed: 6, context: html, text, full: html, text
Splitting out RNA-seq PolyA tails into separate composte in Expression group
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRNAseq.html
- 1.1 lines changed: 163, context: html, text, full: html, text
Splitting out RNA-seq PolyA tails into separate composte in Expression group
- src/hg/makeDb/trackDb/human/wgEncodeGencode.html
- 1.3 lines changed: 52, context: html, text, full: html, text
A bunch of color changes.
- 1.2 lines changed: 1, context: html, text, full: html, text
This is the third release July 2009
- 1.1 lines changed: 198, context: html, text, full: html, text
Moved hg18/wgEnoceSangerGencode to human/wgEncodeGencode for V3 and above. (Sanger left at 18 for rel2)
- src/hg/makeDb/trackDb/lowelab/trackDb.ra
- 1.83 lines changed: 1, context: html, text, full: html, text
changing prediction color
- 1.82 lines changed: 5, context: html, text, full: html, text
adding aligned features color
- 1.81 lines changed: 123, context: html, text, full: html, text
adding colors and combining operons
- src/hg/makeDb/trackDb/mouse/mm9/NIAGene.html
- 1.1 lines changed: 30, context: html, text, full: html, text
Added NIAGene.html for mm9.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- 1.58 lines changed: 12, context: html, text, full: html, text
Added NIAGene for mm9.
- 1.57 lines changed: 1, context: html, text, full: html, text
Changed colour for vega genes to distinguish them more clearly from the pseudogenes subtrack.
- 1.56 lines changed: 1, context: html, text, full: html, text
Added vegaPep table to vegaGeneComposite track entry.
- src/hg/makefile
- 1.153 lines changed: 1, context: html, text, full: html, text
add encode/validateFiles to utils. THis probably should be part of something ENCODE specific (or maybe not).
- src/hg/utils/mysql/dev40ToDev50.csh
- 1.2 lines changed: 1, context: html, text, full: html, text
fix example
- 1.1 lines changed: 50, context: html, text, full: html, text
Initial sources derived from the beta to beta script
- src/hg/utils/mysql/dumpDev40.csh
- 1.3 lines changed: 1, context: html, text, full: html, text
How about a generic location ?
- 1.2 lines changed: 2, context: html, text, full: html, text
different location for .hg.dev40.conf
- 1.1 lines changed: 53, context: html, text, full: html, text
Initial source derived from dumpBeta40.csh
- src/hg/utils/mysql/loadDev50.csh
- 1.1 lines changed: 99, context: html, text, full: html, text
Initial sources derived from the beta to beta script
- src/inc/dnaMotif.h
- 1.4 lines changed: 8, context: html, text, full: html, text
added option to control minimum height of a sequence logo column
- src/lib/dnaMotif.c
- 1.5 lines changed: 18, context: html, text, full: html, text
added option to control minimum height of a sequence logo column
- src/lib/htmshell.c
- 1.64 lines changed: 10, context: html, text, full: html, text
Turns out OK jpg is not needed. Using 'button' tag
- src/utils/bigBedSummary/bigBedSummary.c
- 1.7 lines changed: 4, context: html, text, full: html, text
Adding udcDir to the command line as an option.
- src/utils/bigBedToBed/bigBedToBed.c
- 1.7 lines changed: 4, context: html, text, full: html, text
Adding udcDir to the command line as an option.
- src/utils/bigWigInfo/bigWigInfo.c
- 1.2 lines changed: 4, context: html, text, full: html, text
Adding udcDir to the command line as an option.
- src/utils/bigWigSummary/bigWigSummary.c
- 1.11 lines changed: 4, context: html, text, full: html, text
Adding udcDir to the command line as an option.
- src/utils/bigWigToBedGraph/bigWigToBedGraph.c
- 1.5 lines changed: 4, context: html, text, full: html, text
Adding udcDir to the command line as an option.
- src/utils/qa/databaseAday.csh
- 1.12 lines changed: 1, context: html, text, full: html, text
oops. misnamed outPath variable
- 1.11 lines changed: 6, context: html, text, full: html, text
added path to filename in chmod statement to stop file-not-found error. reduced size of test for proper input parameters
- src/utils/qa/genbankRun.csh
- 1.3 lines changed: 2, context: html, text, full: html, text
fixed updateTimes.csh to work with msyql v5.0 dumps. also simplified the way it works, removing some of the flexibily seldom used. changed call in genbankRun.csh to use new version.
- src/utils/qa/getRRdumpfile.csh
- 1.4 lines changed: 17, context: html, text, full: html, text
fixed updateTimes.csh to work with msyql v5.0 dumps. also simplified the way it works, removing some of the flexibily seldom used. changed call in genbankRun.csh to use new version.
- src/utils/qa/getRRtableStatus.csh
- 1.12 lines changed: 20, context: html, text, full: html, text
fixed updateTimes.csh to work with msyql v5.0 dumps. also simplified the way it works, removing some of the flexibily seldom used. changed call in genbankRun.csh to use new version.
- src/utils/qa/makeTouchCommands.csh
- 1.4 lines changed: 1, context: html, text, full: html, text
clarified usage statement per Ann
- src/utils/qa/updateTimes.csh
- 1.26 lines changed: 1, context: html, text, full: html, text
added host to get beta result properly
- 1.25 lines changed: 101, context: html, text, full: html, text
fixed updateTimes.csh to work with msyql v5.0 dumps. also simplified the way it works, removing some of the flexibily seldom used. changed call in genbankRun.csh to use new version.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/buildHgCentralSql.csh
- 1.17 lines changed: 27, context: html, text, full: html, text
no need for a push request to hgdownload, we can do it ourselves
- src/utils/qa/weeklybld/doZip.csh
- 1.10 lines changed: 9, context: html, text, full: html, text
getting rid of silly hgdownload1 and 2 when we just need one plain instance hgdownload
- lines changed: 6713
- files changed: 114