CVS changes by file
branch to review (2009-09-29 to 2009-10-06) v217
- java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
- 1.3 lines changed: 1, context: html, text, full: html, text
Updated to point to current mysqlbeta.
- src/hg/archaeStuff/data/Genome-info-mods
- 1.85 lines changed: 1, context: html, text, full: html, text
fix Name_chg again
- 1.84 lines changed: 1, context: html, text, full: html, text
add Name_chg to desuKamc1
- 1.83 lines changed: 35, context: html, text, full: html, text
change methFerv0 to methFerv1; add public multiz for halos to exclude natrMaga0; add info for haloUtah1
- 1.82 lines changed: 2, context: html, text, full: html, text
remove pyroOgun03 from public multiz of therPend1
- src/hg/archaeStuff/data/private-genomes.tab
- 1.1 lines changed: 32, context: html, text, full: html, text
list of private genomes in alt browser - to be used by make-browser
- src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
- 1.43 lines changed: 5, context: html, text, full: html, text
fix description page with slash in abstract
- 1.42 lines changed: 8, context: html, text, full: html, text
sync everything from archtest to public
- src/hg/archaeStuff/scripts/archaeBrowser/ProteinStructure.pm
- 1.3 lines changed: 1, context: html, text, full: html, text
fixed Pfam load by Todd
- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
- 1.19 lines changed: 34, context: html, text, full: html, text
implement Angie's suggestions to make the code more readable
- 1.18 lines changed: 2, context: html, text, full: html, text
fix for 32bit
- src/hg/bedSplitOnChrom/bedSplitOnChrom.c
- 1.4 lines changed: 7, context: html, text, full: html, text
add append option to add to, rather than create files
- src/hg/encode/DAFs/UMassTfbsAll.daf
- 1.1 lines changed: 22, context: html, text, full: html, text
Weng lab ENCODE data agreement
- src/hg/encode/DAFs/UMassTfbsAll.ddf
- 1.1 lines changed: 2, context: html, text, full: html, text
Weng lab ENCODE data agreement
- src/hg/encode/DAFs/UMassTfbsValid.daf
- 1.2 lines changed: 1, context: html, text, full: html, text
Add SQL schema
- 1.1 lines changed: 20, context: html, text, full: html, text
Weng lab ENCODE data agreement
- src/hg/encode/DAFs/UMassTfbsValid.ddf
- 1.1 lines changed: 2, context: html, text, full: html, text
Weng lab ENCODE data agreement
- src/hg/encode/DAFs/UwDgf.daf
- 1.1 lines changed: 56, context: html, text, full: html, text
Initial version of UW Digital Genomic Footprinting DAF
- src/hg/encode/converters/tagToBed12/tagToBed12.c
- 1.2 lines changed: 1, context: html, text, full: html, text
put X in missing 14th field
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- 1.71 lines changed: 4, context: html, text, full: html, text
Add support for 'sql' field in DAF. Allows specifying the schema for a non-standard table. The .sql file needs to be copied to /cluster/bin//sqlCreate
- src/hg/encode/encodeValidate/config/cv.ra
- 1.133 lines changed: 1, context: html, text, full: html, text
Sorry changing NFkB back to NFKB as this seems to be a valid term in the literature
- 1.132 lines changed: 40, context: html, text, full: html, text
For Yale added NF-YA and NF-YB and renamed NFKB to NFkB
- 1.131 lines changed: 15, context: html, text, full: html, text
Added antibody NFKB and treatment TNFa for Yale.
- src/hg/encode/encodeValidate/config/fields.ra
- 1.20 lines changed: 5, context: html, text, full: html, text
Add DAF support for listing sql schema for custom bed file
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- 1.196 lines changed: 4, context: html, text, full: html, text
Add support for 'sql' field in DAF. Allows specifying the schema for a non-standard table. The .sql file needs to be copied to /cluster/bin//sqlCreate
- 1.195 lines changed: 4, context: html, text, full: html, text
Support bed3s
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- 1.27 lines changed: 1, context: html, text, full: html, text
Oops, introduced a new fputs w/no return value -- thanks Brian for catching in review.
- src/hg/encode/validateFiles/validateFiles.c
- 1.28 lines changed: 1, context: html, text, full: html, text
fix narrowPeak check to actually use the peak rather than the score
- src/hg/gsid/gsidTable/gsidTable.c
- 1.50 lines changed: 1, context: html, text, full: html, text
Take out a break. Ann does not like it and Fan forgot why he put it in.
- src/hg/hgGenome/import.c
- 1.15 lines changed: 45, context: html, text, full: html, text
adding work-around to genome graphs import for bedgraph customtracks, also some elimination of unneeded connection variable
- src/hg/hgTracks/bedTrack.c
- 1.17 lines changed: 4, context: html, text, full: html, text
colorByStrand for bed12's
- src/hg/hgc/hgc.c
- 1.1577 lines changed: 6, context: html, text, full: html, text
fixup access to normScore column for tables that have that
- src/hg/instinct/bioInt2/bioIntDriver.h
- 1.9 lines changed: 1, context: html, text, full: html, text
Fixed compile warnings
- src/hg/instinct/bioInt2/bioPathway.h
- 1.3 lines changed: 3, context: html, text, full: html, text
Fixed compile warnings
- src/hg/instinct/bioInt2/bioPathwayLevel.c
- 1.7 lines changed: 3, context: html, text, full: html, text
Fixed compile warnings
- src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
- 1.4 lines changed: 9, context: html, text, full: html, text
Fixed compile warnings
- src/hg/instinct/hgHeatmap2/drawingCode.c
- 1.75 lines changed: 3, context: html, text, full: html, text
add code doc for modified drawing code
- 1.74 lines changed: 7, context: html, text, full: html, text
fix snp summary view
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
- 1.25 lines changed: 1, context: html, text, full: html, text
Fixed naderi probe table
- 1.24 lines changed: 1, context: html, text, full: html, text
Fixed target cnv probe table
- src/hg/lib/immuno.sql
- 1.1 lines changed: 15, context: html, text, full: html, text
Created immuno.sql for GSID immuno data.
- src/hg/lib/immunoRaw.sql
- 1.1 lines changed: 15, context: html, text, full: html, text
Create immunoRaw.sql to be used on building immuno related data for GSID TB.
- src/hg/lib/webUsers.sql
- 1.1 lines changed: 12, context: html, text, full: html, text
Create webUsers.sql to be used by webUserAdmin.
- src/hg/lib/wigAsciiToBinary.c
- 1.33 lines changed: 19, context: html, text, full: html, text
Reverting Hiram's changes temporarily, since ENCODE pipeline is now failing validation left and right
- 1.32 lines changed: 2, context: html, text, full: html, text
A bit too agressive on that overlap check, don't do it for position 0
- 1.31 lines changed: 19, context: html, text, full: html, text
Was missing overlapping data condition on a fixedStep case
- src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
- 1.5 lines changed: 121, context: html, text, full: html, text
Finished up the Sep 2009 freeze submissions with Melissa's help
- src/hg/makeDb/doc/encodeDccHg18/gencode.txt
- 1.3 lines changed: 336, context: html, text, full: html, text
Thought I should check in old stuff done for Gencode Release 3. Two issues still unresolved, though
- src/hg/makeDb/doc/encodeDccHg18/myers.txt
- 1.3 lines changed: 46, context: html, text, full: html, text
Tim adds some preliminary notes. No activity seen for Sept 2009 freeze
- src/hg/makeDb/doc/encodeDccHg18/nhgriNreBipElnitski.txt
- 1.3 lines changed: 17, context: html, text, full: html, text
Finally checking in some antient notes
- src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
- 1.1 lines changed: 253, context: html, text, full: html, text
Added a lot of ChIPseq and DNase as part of the Sept 2009 freeze. Tracy Ballinger helped with trackDb, fileDb
- src/hg/makeDb/doc/hg19.txt
- 1.42 lines changed: 25, context: html, text, full: html, text
remade grep table in include new column and split reg from expr
- 1.41 lines changed: 102, context: html, text, full: html, text
Doing stuff to get gnfAtlas2 data in.
- 1.40 lines changed: 31, context: html, text, full: html, text
Adding Allen Brain track to hg19.
- src/hg/makeDb/doc/hivVax003Vax004.txt
- 1.9 lines changed: 38, context: html, text, full: html, text
Added the section of immuno build.
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
- 1.6 lines changed: 14, context: html, text, full: html, text
Did old to new mapping.
- 1.5 lines changed: 12, context: html, text, full: html, text
Making a few more knownTo tables
- 1.4 lines changed: 36, context: html, text, full: html, text
Doing/redoing some knownTo tables and pfam.
- src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
- 1.1 lines changed: 1206, context: html, text, full: html, text
Starting new build of mouse UCSC Genes.
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- 1.99 lines changed: 1, context: html, text, full: html, text
Added new elephant.
- src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
- 1.91 lines changed: 1, context: html, text, full: html, text
Fixed TARGET cnv ids to match exp
- src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
- 1.15 lines changed: 2, context: html, text, full: html, text
Adding a little more detail to history table record of hgLoadSeq. It still is giving warnings, I think maybe because of the missing gbDate field.
- src/hg/makeDb/trackDb/README
- 1.88 lines changed: 6, context: html, text, full: html, text
added two variables
- src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
- 1.12 lines changed: 5, context: html, text, full: html, text
grouping hg18 and hg19 chainnets together
- 1.11 lines changed: 1, context: html, text, full: html, text
fixed chain o_db override in shortLabel to say chain, not net
- src/hg/makeDb/trackDb/human/dgv.html
- 1.5 lines changed: 3, context: html, text, full: html, text
Made the color explanation more clear (thx Pauline).
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- 1.563 lines changed: 15, context: html, text, full: html, text
Modified the tags for the factors for the Broad tracks so that the subtracks
appear in proper alphabetical order.
- 1.562 lines changed: 67, context: html, text, full: html, text
fix up some long labels for AffyRna and other tracks
qVS: ----------------------------------------------------------------------
- 1.561 lines changed: 35, context: html, text, full: html, text
Finxed HeLa and HepG2 sort order in UW Dnase and ChIP
- 1.560 lines changed: 1179, context: html, text, full: html, text
Did some Broad track reordering
- 1.559 lines changed: 31, context: html, text, full: html, text
Left out UW ChIP HUVEC CTCF rep1 from last night's checkins
- 1.558 lines changed: 146, context: html, text, full: html, text
Its ChIP-seq not ChIP-Seq
- 1.557 lines changed: 1027, context: html, text, full: html, text
Reorganized UW DNase
- 1.556 lines changed: 3, context: html, text, full: html, text
Removed stray bad line. Changed UW DNase raw sig view range
- 1.555 lines changed: 1514, context: html, text, full: html, text
Added UW ChIPseq nad UW DNase. Reorganized a little
- 1.554 lines changed: 577, context: html, text, full: html, text
Added new Broad histone chip-seq data
- 1.553 lines changed: 4, context: html, text, full: html, text
turn on GM12878 nlos by default in Affy RNA loc track
- 1.552 lines changed: 2, context: html, text, full: html, text
small fix, npls to nplm in Affy RNA loc track
- 1.551 lines changed: 105, context: html, text, full: html, text
fix up short labels for Affy RNA loc track
- 1.550 lines changed: 426, context: html, text, full: html, text
take out commented out old CSHL short RNA-seq entries
- 1.549 lines changed: 4, context: html, text, full: html, text
add color to CSHL Long RNA-seq track
- 1.548 lines changed: 241, context: html, text, full: html, text
new CSHL long RNA-seq setup
- 1.547 lines changed: 1, context: html, text, full: html, text
adding some color
- 1.546 lines changed: 1, context: html, text, full: html, text
changing dataVersion to include Sep 09 freeze
- src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
- 1.16 lines changed: 3, context: html, text, full: html, text
Wording improvement in collaboration with braney.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
- 1.37 lines changed: 3, context: html, text, full: html, text
removing types that are no longer going to be part of this track
- src/hg/makeDb/trackDb/human/hg19/snp130.html
- 1.1 lines changed: 257, context: html, text, full: html, text
Make it clear that this is a provisional release, based on the hg18 data files but w/mapping to hg19 coords from dbSNP.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- 1.53 lines changed: 7, context: html, text, full: html, text
moved venter and his dog out of the way of the main chainNet tracks
- 1.52 lines changed: 37, context: html, text, full: html, text
moved all the overrides together
- src/hg/makeDb/trackDb/lamprey/trackDb.ra
- 1.4 lines changed: 9, context: html, text, full: html, text
set hg18 chainnets to o_db
- src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
- 1.16 lines changed: 1, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/halMar1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
- 1.17 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.16 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/haloHalo1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
- 1.21 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.20 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/haloSali1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
- 1.11 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.10 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/haloUtah1/multizHalophiles.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloUtah1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloUtah1/trackDb.ra
- 1.3 lines changed: 17, context: html, text, full: html, text
Update multiz track
- 1.2 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/haloVolc1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloVolc1/trackDb.ra
- 1.8 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.7 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/haloWals1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
- 1.13 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.12 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/igenics.html
- src/hg/makeDb/trackDb/lowelab/igenicsMicroarray.html
- 1.1 lines changed: 4, context: html, text, full: html, text
rename track and file
- src/hg/makeDb/trackDb/lowelab/methInfe0/multizMethanococcus.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/methInfe0/trackDb.ra
- src/hg/makeDb/trackDb/lowelab/methJann1/trackDb.ra
- 1.15 lines changed: 1, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/methVulc0/trackDb.ra
- src/hg/makeDb/trackDb/lowelab/natrPhar1/multizHalophilesPriv.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
- 1.13 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.12 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/privateTracks.ra
- 1.20 lines changed: 14, context: html, text, full: html, text
add private multiz, RNA and sequencing tracks
- src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
- 1.27 lines changed: 1, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/pyroCali1/trackDb.ra
- 1.29 lines changed: 1, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
- 1.30 lines changed: 1, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/therNeut1/multizPbacCmaTpe.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/therNeut1/trackDb.ra
- 1.10 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/therPend1/description.html
- 1.6 lines changed: 2, context: html, text, full: html, text
Added isolation paper info.
- src/hg/makeDb/trackDb/lowelab/therPend1/multizPbacCmaTpe.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/therPend1/trackDb.ra
- 1.12 lines changed: 4, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/lowelab/vulcDist0/multizPbacVdiCmaTpe.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/vulcDist0/trackDb.ra
- 1.7 lines changed: 1, context: html, text, full: html, text
Update multiz track
- 1.6 lines changed: 17, context: html, text, full: html, text
Update multiz track
- 1.5 lines changed: 17, context: html, text, full: html, text
Update multiz track
- src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
- 1.9 lines changed: 1, context: html, text, full: html, text
Fixed date on canFam2.
- src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
- 1.12 lines changed: 1, context: html, text, full: html, text
fixed chain db override in sortLabel to say chain, not net
- src/hg/makeDb/trackDb/stickleback/trackDb.ra
- 1.17 lines changed: 13, context: html, text, full: html, text
set hg18 chainnets to o_db and adjusted priority of chainNetHg19
- src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
- 1.3 lines changed: 9, context: html, text, full: html, text
set override on chain and net hg18 to o_db
- src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
- 1.9 lines changed: 1, context: html, text, full: html, text
Fixed typo in comment
- src/hg/tcga/bamBam/bamBam.c
- 1.8 lines changed: 8, context: html, text, full: html, text
finally fixed terrible bug, implemented seeking
- 1.7 lines changed: 383, context: html, text, full: html, text
updated
- 1.6 lines changed: 472, context: html, text, full: html, text
updated
- src/hg/tcga/bamBam/bam_dual_pileup.c
- 1.6 lines changed: 190, context: html, text, full: html, text
finally fixed terrible bug, implemented seeking
- 1.5 lines changed: 1, context: html, text, full: html, text
fixed a terrible, terrible bug
- src/hg/tcga/bamBam/bam_dual_pileup.h
- 1.4 lines changed: 2, context: html, text, full: html, text
finally fixed terrible bug, implemented seeking
- src/hg/tcga/bamFindPairs/bamFindPairs.c
- src/hg/tcga/bamFindPairs/makefile
- src/hg/txGene/txGeneAddOldUnmapped/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
Utility to add in genes that couldn't be mapped from previous assembly to oldToNew table seems to work.
- src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
- 1.1 lines changed: 67, context: html, text, full: html, text
Utility to add in genes that couldn't be mapped from previous assembly to oldToNew table seems to work.
- src/hg/txGene/txGeneExplainUpdate2/txGeneExplainUpdate2.c
- 1.2 lines changed: 22, context: html, text, full: html, text
Adding -unmapped and -oldAsm options.
- src/hg/utils/automation/Encode.pm
- 1.47 lines changed: 1, context: html, text, full: html, text
Add custom bed schema for Weng lab
- src/hg/utils/automation/doHgNearBlastp.pl
- 1.11 lines changed: 1, context: html, text, full: html, text
Made it treat 'tmpFoo' as a mammal for updates in place of the database.
- src/lib/bwgCreate.c
- 1.17 lines changed: 3, context: html, text, full: html, text
Improving error message.
- src/utils/qa/idHitter.csh
- 1.1 lines changed: 66, context: html, text, full: html, text
checking in script to find out what a heavy hitter is doing
- src/utils/qa/weeklybld/buildEnv.csh
- 1.82 lines changed: 2, context: html, text, full: html, text
v217 preview
- 1.81 lines changed: 1, context: html, text, full: html, text
new better location without tmp stigma
- src/utils/qa/weeklybld/doHgTablesTestRobot.csh
- src/utils/qa/weeklybld/doNewBranch.csh
- 1.31 lines changed: 2, context: html, text, full: html, text
cvs reports fixing email msg on cvsreports ready
- src/utils/qa/weeklybld/doNewReview.csh
- 1.16 lines changed: 1, context: html, text, full: html, text
cvs reports fixing email msg on cvsreports ready
- lines changed: 12203
- files changed: 108