All File Changes
v263_preview to v263_preview2 (2012-01-31 to 2011-02-07) v263
- python/lib/ucscgenomics/cv.py
- lines changed 42, context: html, text, full: html, text
added optional label for all stanzas in CV, and dataGroup mandatory for dataType
- python/lib/ucscgenomics/geo.py
- lines changed 1, context: html, text, full: html, text
cvValidate updated for new cv spec
- python/lib/ucscgenomics/mdb.py
- lines changed 47, context: html, text, full: html, text
cvValidate updated for new cv spec
- python/lib/ucscgenomics/qa.py
- lines changed 3, context: html, text, full: html, text
added in snippet to detect if a label is still autogenerated
- python/lib/ucscgenomics/ra.py
- lines changed 42, context: html, text, full: html, text
reversing morgan's merge, and adding back in his comments
- python/programs/cvValidate/cvValidate
- lines changed 1, context: html, text, full: html, text
added optional label for all stanzas in CV, and dataGroup mandatory for dataType
- lines changed 0, context: html, text, full: html, text
cvValidate updated for new cv spec
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassDekker5C.daf
- lines changed 24, context: html, text, full: html, text
Updated DAF to have all views. Added new view PrimerPeaks for Peaks determined at primer level. Also added validte None for Primer. Redmine #225.
- lines changed 6, context: html, text, full: html, text
Removed required tags in the DAF, this allows for views such as Primers not being required for each Cell type. Also fixed spelling of bed 12. Redmine #225.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
- lines changed 2, context: html, text, full: html, text
Fixed DAF to require replciates for Alignments. Redmine #4156.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
- lines changed 14, context: html, text, full: html, text
Added two new views Contigs and TranscriptDeNovo. Redmine #5986.
- lines changed 8, context: html, text, full: html, text
Removed required for views to allow partial submissions. Redmine #5986.
- lines changed 2, context: html, text, full: html, text
After tallking with the lab decided to changed type for contigs from bigBed to bedRnaElements. Redmine #5986.
- src/hg/encode/autoSql/bedRrbs.as
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- lines changed 47, context: html, text, full: html, text
bigBed loading ability added in
- src/hg/encode/encodeLoad/doEncodeUnload.pl
- lines changed 26, context: html, text, full: html, text
bigBed loading ability added in
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 1, context: html, text, full: html, text
Added None as a valid term for region, as some files are not region specific. Redmine #225.
- src/hg/hgGene/hgGeneData/Rat/genome.ra
- lines changed 1, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/Rat/links.ra
- lines changed 10, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/Rat/rn3/genome.ra
- lines changed 6, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/Rat/rn4/genome.ra
- lines changed 7, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
- lines changed 92, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/Rat/rn4/section.ra
- lines changed 12, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/hgGeneData/otherOrgs.ra
- lines changed 1, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/pathways.c
- lines changed 1, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/hgGene/synonym.c
- lines changed 19, context: html, text, full: html, text
addComma becomes addCommaSpace
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 19, context: html, text, full: html, text
Added data format info to the form labels and got rid of the ata formats box since it was redunant.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 11, context: html, text, full: html, text
Fix some edge cases when superChild composite is hidden by its superParent. Redmine 6622
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
hTableExists fails when the db does not exist, eliminate dependency on hgFixed existing for cutters data from hgFixed and trackVersion table in hgFixed
- src/hg/hgTracks/vcfTrack.c
- lines changed 6, context: html, text, full: html, text
move knetUdcInstall to other version of vcfTabixMethods to fix #6782
- src/hg/hgTracks/wigTrack.c
- lines changed 14, context: html, text, full: html, text
when autoscaling and the range is 0 (ie. all values are the same), add one to the range so a bar is drawn (#6763)
- src/hg/hgc/hgc.c
- lines changed 4, context: html, text, full: html, text
different location to avoid duplicate html page for custom track bedDetail
- lines changed 1, context: html, text, full: html, text
removed extra / in the url to cloneDb based on review #6785 feedback
- src/hg/htdocs/FAQ/FAQmaillist.html
- lines changed 7, context: html, text, full: html, text
Included link for mailing list guidelines and made FAQ more up to date
- lines changed 1, context: html, text, full: html, text
Changed link to open in new tab
- src/hg/htdocs/goldenPath/help/bigBed.html
- lines changed 1, context: html, text, full: html, text
name of script was changed
- src/hg/htdocs/goldenPath/help/bigWig.html
- lines changed 2, context: html, text, full: html, text
name of script was changed
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 383, context: html, text, full: html, text
Removed BED, PSL, GFF, GTF and Microarray sections. All references now point to the equivalent sections in FAQ/FAQformat.html.
- src/hg/htdocs/goldenPath/help/cutters.html
- lines changed 1, context: html, text, full: html, text
Added the class stdTbl to the table so the borders would display properly
- src/hg/htdocs/goldenPath/help/hgTablesHelp.html
- lines changed 58, context: html, text, full: html, text
Added section for Correlation function
- src/hg/htdocs/goldenPath/help/iupac.html
- lines changed 1, context: html, text, full: html, text
Added the class stdTbl to the table so the borders would display properly
- src/hg/htdocs/goldenPath/help/qValue.html
- lines changed 1, context: html, text, full: html, text
Added missing punctuation
- src/hg/htdocs/indexNews.html
- lines changed 60, context: html, text, full: html, text
Added announcement for new hg19 UCSC Genes track.
- src/hg/htdocs/staff.html
- lines changed 84, context: html, text, full: html, text
Updated people + content.
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
For unknown reasons IE8 fails to find '#pop' occasionally. This fixes 6723
- src/hg/js/hui.js
- lines changed 4, context: html, text, full: html, text
Fix some edge cases when superChild composite is hidden by its superParent. Redmine 6622
- src/hg/js/subCfg.js
- lines changed 3, context: html, text, full: html, text
Fix some edge cases when superChild composite is hidden by its superParent. Redmine 6622
- src/hg/lib/customFactory.c
- lines changed 21, context: html, text, full: html, text
turn off bam/big* chrom size checking code because so many users have big* files with invalid chrom sizes; may turn this error to a warning in the future
- src/hg/lib/ensFace.c
- lines changed 1, context: html, text, full: html, text
hTableExists fails when the db does not exist, eliminate dependency on hgFixed existing for cutters data from hgFixed and trackVersion table in hgFixed
- src/hg/lib/hVarSubst.c
- lines changed 9, context: html, text, full: html, text
add a capability to automatically generate a link to the Assembly Gateway page. #6237
- src/hg/lib/hdb.c
- lines changed 2, context: html, text, full: html, text
MLQ #6823:In hGetChromInfo, if chrom name is implausibly long, just return NULL
(i.e. not a valid chrom name) so we don't pointlessly safef -> errAbort.
- src/hg/lib/hgFind.c
- lines changed 4, context: html, text, full: html, text
Track #29 (Shift rat to RGD gene set): fixed hole in hgFind.c logicthat caused IDs like "RGD:3136" to have single-base position ranges
in results.
- src/hg/lib/hui.c
- lines changed 11, context: html, text, full: html, text
Subtracks were sometimes seen in the image even though they are not checked. Fix for redmine 2375
- src/hg/makeDb/doc/bosTau7.txt
- lines changed 69, context: html, text, full: html, text
Finished chainNet between bosTau7 and ornAna1
- src/hg/makeDb/doc/canFam2.txt
- lines changed 3, context: html, text, full: html, text
Added some build notes for the PolyA-Seq track
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
- lines changed 31, context: html, text, full: html, text
updated notes for haib tfbs
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release3.notes
- lines changed 2370, context: html, text, full: html, text
first pass at notes for histone
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release3.notes
- lines changed 1635, context: html, text, full: html, text
first pass at release 3 notes for uw tfbs
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 83, context: html, text, full: html, text
Finish hetG;a1 genscan task.
- src/hg/makeDb/doc/hg18.txt
- lines changed 5, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update. hg19 now uses snp135.
- src/hg/makeDb/doc/hg19.txt
- lines changed 20, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update. hg19 now uses snp135.
- lines changed 62, context: html, text, full: html, text
Added some build notes for the PolyA-Seq track
- src/hg/makeDb/doc/mm10.txt
- lines changed 534, context: html, text, full: html, text
starting mm10, now running repeat masker and window masker, simple repeats are done
- src/hg/makeDb/doc/mm9.txt
- lines changed 4, context: html, text, full: html, text
Added some build notes for the PolyA-Seq track
- src/hg/makeDb/doc/ornAna1.txt
- lines changed 11, context: html, text, full: html, text
Finished chainNet between bosTau7 and ornAna1
- src/hg/makeDb/doc/rheMac2.txt
- lines changed 4, context: html, text, full: html, text
Added some build notes for the PolyA-Seq track
- src/hg/makeDb/doc/rn4.txt
- lines changed 217, context: html, text, full: html, text
cleaning rgdGene2ToUniProt table
- lines changed 118, context: html, text, full: html, text
cleaning old instructions for cleaning rgdGene2ToUniProt table
- lines changed 3, context: html, text, full: html, text
Added some build notes for the PolyA-Seq track
- src/hg/makeDb/doc/sarHar1.txt
- lines changed 216, context: html, text, full: html, text
Initial sarHar1 (Tasmanian devil) browser build.
- src/hg/makeDb/doc/tRNAsTrack.txt
- lines changed 4, context: html, text, full: html, text
Add function to reload tRNAs table. redmine bug 6831
- src/hg/makeDb/schema/all.joiner
- lines changed 22, context: html, text, full: html, text
Changing comments ot be inline
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 27, context: html, text, full: html, text
Adding typeofTerm for organism and dataGroup, I am not sure why they did not have one.
- lines changed 7, context: html, text, full: html, text
Updated DAF to have all views. Added new view PrimerPeaks for Peaks determined at primer level. Also added validte None for Primer. Redmine #225.
- lines changed 115, context: html, text, full: html, text
added new validation doc references and new antibodies
- lines changed 12, context: html, text, full: html, text
correcting some errors found in willy's comment shuffling
- lines changed 1, context: html, text, full: html, text
correcting an incorrect key name
- lines changed 18, context: html, text, full: html, text
Added 3 new treatments for Snyder/Struhl lab
- lines changed 6, context: html, text, full: html, text
Removed the duplication of a 36hr 1 uM treatment registration.
- lines changed 36, context: html, text, full: html, text
fixed per code review issue #6784
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 6, context: html, text, full: html, text
Removed extra stanza that should be commented out. Redmine #6798.
- src/hg/makeDb/trackDb/dog/canFam2/polyASeqSites.html
- lines changed 78, context: html, text, full: html, text
Added polyASeq to canFam2 browser
- src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
- lines changed 74, context: html, text, full: html, text
Added polyASeq to canFam2 browser
- src/hg/makeDb/trackDb/human/dgv.html
- lines changed 5, context: html, text, full: html, text
Updated deprecated font tags to css; should also fix color error reported on WinXP/FF3.6 - font tag colors weren't even formatted correctly.
- src/hg/makeDb/trackDb/human/hg19/knownGene.html
- lines changed 148, context: html, text, full: html, text
Removed release tags from knownGene track, moved knownGeneNew.html to knownGene.html for release of new version of UCSC Genes.
- lines changed 0, context: html, text, full: html, text
Added a space after a comma.
- src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
- lines changed 160, context: html, text, full: html, text
Removed release tags from knownGene track, moved knownGeneNew.html to knownGene.html for release of new version of UCSC Genes.
- src/hg/makeDb/trackDb/human/hg19/knownGeneOld5.html
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 309, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 435, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 74, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 89, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- lines changed 2, context: html, text, full: html, text
Corrections based on ticket 5942 note 16
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
- lines changed 1, context: html, text, full: html, text
Adding labVersion as a expId
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 51, context: html, text, full: html, text
added in metadata for replacement peaks SL1655 and SL1507
- lines changed 3, context: html, text, full: html, text
added in md5sums for the replacement files
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 123, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 15, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.ra
- lines changed 3, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 33, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 309, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
- lines changed 430, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
- lines changed 67, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromSynth.ra
- lines changed 227, context: html, text, full: html, text
Staging Open Chrom Synth on beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 123, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProt.ra
- lines changed 15, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
- lines changed 33, context: html, text, full: html, text
updated cricket's tracks with the final freeze dates, staged to beta
- src/hg/makeDb/trackDb/human/hg19/polyASeqSites.html
- lines changed 102, context: html, text, full: html, text
trackDb for polyASeq track
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 32, context: html, text, full: html, text
Removed release tags from knownGene track, moved knownGeneNew.html to knownGene.html for release of new version of UCSC Genes.
- lines changed 171, context: html, text, full: html, text
trackDb for polyASeq track
- lines changed 6, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update. hg19 now uses snp135.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
adding in alpha tag and release3 ra for uw tfbs
- lines changed 2, context: html, text, full: html, text
Corrections based on ticket 5942 note 16
- lines changed 2, context: html, text, full: html, text
added in alpha tag to new release3 .ra Riken cAge
- lines changed 2, context: html, text, full: html, text
Staging Open Chrom Synth on beta
- lines changed 2, context: html, text, full: html, text
Beginning a new release for this track and adding views
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
- lines changed 11, context: html, text, full: html, text
Making changes on subgroup tags according to Tim and Katrina feedback, trying to force order without using numerals
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
- lines changed 32, context: html, text, full: html, text
Corrections based on ticket 5942 note 16
- lines changed 14, context: html, text, full: html, text
Further changes according to pre-QA
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
- lines changed 3, context: html, text, full: html, text
Corrections based on ticket 5942 note 16
- lines changed 2, context: html, text, full: html, text
Further changes according to pre-QA
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
- lines changed 32, context: html, text, full: html, text
added in replacement tracks for SL1655 and SL1507
- lines changed 2, context: html, text, full: html, text
pre-qa fixes for .ra files haib tfbs
- lines changed 31, context: html, text, full: html, text
self merge to balance whitespace
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
- lines changed 160, context: html, text, full: html, text
moving files to release tagged structure
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 1, context: html, text, full: html, text
making it so that plus and minus have the same draw window
- lines changed 1, context: html, text, full: html, text
fixed short label to be consistent
- lines changed 2209, context: html, text, full: html, text
moving files to release tagged structure
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html
- lines changed 160, context: html, text, full: html, text
moving files to release tagged structure
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
- lines changed 2209, context: html, text, full: html, text
moving files to release tagged structure
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 24, context: html, text, full: html, text
Beginning a new release for this track and adding views
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
- lines changed 1, context: html, text, full: html, text
more accurate release note
- lines changed 3, context: html, text, full: html, text
added in snippet about all objects having an FDR of 1%
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
- lines changed 669, context: html, text, full: html, text
long labels for uw histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
- lines changed 94, context: html, text, full: html, text
html for release 3 uw tfbs
- lines changed 1, context: html, text, full: html, text
fixed misspelling for month
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
- lines changed 578, context: html, text, full: html, text
long labels for uw tfbs
- lines changed 15, context: html, text, full: html, text
last commit should have said cleaning up UwTfbs trackDb release 3
- lines changed 8, context: html, text, full: html, text
wgEncodeUwTfbs.release3.ra
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 12, context: html, text, full: html, text
add a copy of cosmic track with release alpha tag
- lines changed 1, context: html, text, full: html, text
add release beta,public to old cosmic stanza
- src/hg/makeDb/trackDb/makefile
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
- lines changed 2, context: html, text, full: html, text
Added first experiments to track. Redmine #4156.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
- lines changed 64, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 210, context: html, text, full: html, text
Added first experiments to track. Redmine #4156.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
- lines changed 124, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 97, context: html, text, full: html, text
Removed WC+ from labProtocolId string, based on lab information. Redmine #5986.
- lines changed 97, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- lines changed 6, context: html, text, full: html, text
Added back composite level meta-data was typed incorrectly in commit 66cb88518473df9e9dbc818fe28bd1eefed69a2e.
- lines changed 6, context: html, text, full: html, text
Removed errant stanza object wgEncodeCshlLongRnaSeqq.
- lines changed 2989, context: html, text, full: html, text
Added 18 experiments for track. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 376, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- lines changed 115, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 248, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 293, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 239, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
- lines changed 28, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 10, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 323, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 85, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 486, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 206, context: html, text, full: html, text
Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging PSU Histone track on beta
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
- lines changed 7920, context: html, text, full: html, text
Staging PSU Histone track on beta
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
- lines changed 239, context: html, text, full: html, text
addding Venkats freeze date changes, redmine# 110 note# 32
- src/hg/makeDb/trackDb/mouse/mm9/polyASeqSites.html
- lines changed 86, context: html, text, full: html, text
Added trackDb for polyASeq for mm9
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 106, context: html, text, full: html, text
Added trackDb for polyASeq for mm9
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Staging PSU Histone track on beta
- lines changed 3, context: html, text, full: html, text
Added first experiments to track. Redmine #4156.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.ra
- lines changed 91, context: html, text, full: html, text
Added first experiments to track. Redmine #4156.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
- lines changed 487, context: html, text, full: html, text
Added 18 experiments for track. Redmine #5986.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
- lines changed 0, context: html, text, full: html, text
added a space in front of (PSU) for PSU TFBS and PSU Histone since they have the same description page.
- lines changed 17, context: html, text, full: html, text
Redmine #111
1. Reworded sentence "and interpret these as DNA sequences" -> "and interpreted as DNA sequences"
2. Added semicolon in second sentence of Peaks section in Display Conventions and Configuration
3. Made Credits section plural changed "was" -> "were"
4. Added period for Journal titles. Also italicized "et al." in Reference section
- lines changed 2, context: html, text, full: html, text
Redmine #111. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
- lines changed 1, context: html, text, full: html, text
Redmine #111. Forgot to close italics.
- lines changed 4, context: html, text, full: html, text
Redmine #111. 5. Updated 2 links that were being redirected.
- lines changed 1, context: html, text, full: html, text
Redmine #111. Moved period out of hyperlink for Weiss track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 19, context: html, text, full: html, text
1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
- lines changed 19, context: html, text, full: html, text
1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
- lines changed 0, context: html, text, full: html, text
added a space in front of (PSU) for PSU TFBS and PSU Histone since they have the same description page.
- lines changed 18, context: html, text, full: html, text
Redmine #110
1. Reworded sentence "and interpret these as DNA sequences" -> "and interpreted as DNA sequences"
2. Added semicolon in second sentence of Peaks section in Display Conventions and Configuration
3. Made Credits section plural changed "was" -> "were"
4. Added period for Journal titles.
- lines changed 5, context: html, text, full: html, text
Redmine #110. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
- src/hg/makeDb/trackDb/rat/rn4/polyASeqSites.html
- lines changed 74, context: html, text, full: html, text
trackDb for polyA-Seq for rat
- src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
- lines changed 22, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
- lines changed 18, context: html, text, full: html, text
checking in rgdGene2 search specs
- lines changed 59, context: html, text, full: html, text
trackDb for polyA-Seq for rat
- lines changed 18, context: html, text, full: html, text
trying to resolve conflict
- lines changed 12, context: html, text, full: html, text
one last bit of catch up for rgdGene2 checkin
- src/hg/makeDb/trackDb/rhesus/rheMac2/polyASeqSites.html
- lines changed 86, context: html, text, full: html, text
Added trackDb to polyASeq for Rhesus
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
- lines changed 106, context: html, text, full: html, text
Added trackDb to polyASeq for Rhesus
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 6, context: html, text, full: html, text
adding bigBed to certain trackDb tags for the new bisulfite track
- lines changed 1, context: html, text, full: html, text
Added first experiments to track. Redmine #4156.
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
- lines changed 132, context: html, text, full: html, text
Initial descriptions for sarHar1.
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/gap.html
- lines changed 64, context: html, text, full: html, text
Initial descriptions for sarHar1.
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/gold.html
- lines changed 23, context: html, text, full: html, text
Initial descriptions for sarHar1.
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
Initial descriptions for sarHar1.
- src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
- lines changed 165, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/near/hgNear/hgNearData/Rat/rn4/genome.ra
- lines changed 10, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/near/hgNear/hgNearData/Rat/rn4/orderDb.ra
- lines changed 27, context: html, text, full: html, text
checking in Fan's branch for the rgdGene2 update
- src/hg/utils/automation/Encode.pm
- lines changed 1, context: html, text, full: html, text
bigBed loading ability added in
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 17, context: html, text, full: html, text
Add two new parameters ncbiAssemblyId and ncbiAssemblyName to generate 'For more information about this assembly, see <XXXXXX> in the NCBI Assembly database.' in the description.html
- lines changed 5, context: html, text, full: html, text
Polish the help message on ncbiAssemblyName and ncbiAssemblyId
- src/lib/bwgQuery.c
- lines changed 5, context: html, text, full: html, text
fix up assert to be accurate, and break out of two loops when we've put out the limit of items (#6851)
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/doNewBranch.csh
- lines changed 7, context: html, text, full: html, text
Tweaked the email checkin summary notice as per Ann's request
- lines changed 7, context: html, text, full: html, text
Ann wanted me to check in the code to send a 'code summary reminder' to all persons who checked in code in this period.
- src/utils/qa/weeklybld/summaryEmail.sh
- lines changed 38, context: html, text, full: html, text
Tweaked the email checkin summary notice as per Ann's request
- lines changed 10, context: html, text, full: html, text
Ann wanted me to check in the code to send a 'code summary reminder' to all persons who checked in code in this period.
- lines changed: 32397
- files changed: 220