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
  • lines changed 2, context: html, text, full: html, text
    Changed capitalization
• 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.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo.
• 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
  • lines changed 7, context: html, text, full: html, text
    added in taxol treatment
• 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
  • lines changed 1, context: html, text, full: html, text
    Added a period.
• 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
  • lines changed 166, context: html, text, full: html, text
    md5sums for Riken
• 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
  • lines changed 11, context: html, text, full: html, text
    expIds and accessions
• 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
  • lines changed 4, context: html, text, full: html, text
    pre-qa fixes
• 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
  • lines changed 2, context: html, text, full: html, text
    pre-qa fixes
• 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%
  • lines changed 4, context: html, text, full: html, text
    pre-qa fixes
  • lines changed 2, context: html, text, full: html, text
    pre-qa fixes again
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 669, context: html, text, full: html, text
    long labels for uw histone
  • lines changed 79, context: html, text, full: html, text
    short labels histone
  • lines changed 1, context: html, text, full: html, text
    pre-qa fixes
• 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 2, context: html, text, full: html, text
    pre-qa fixes again
  • 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
  • lines changed 1, context: html, text, full: html, text
    Added sarHar1 to DBS.
• 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.
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
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    Added back composite level meta-data was typed incorrectly in commit 66cb88518473df9e9dbc818fe28bd1eefed69a2e.
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    Removed errant stanza object wgEncodeCshlLongRnaSeqq.
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    Added 18 experiments for track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
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    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
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    Staging PSU Histone track on beta
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
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    Staging PSU Histone track on beta
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
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    addding Venkats freeze date changes, redmine# 110 note# 32
• src/hg/makeDb/trackDb/mouse/mm9/polyASeqSites.html
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    Added trackDb for polyASeq for mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
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    Added trackDb for polyASeq for mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
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    Staging PSU Histone track on beta
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    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.ra
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    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
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    Added 18 experiments for track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
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    added a space in front of (PSU) for PSU TFBS and PSU Histone since they have the same description page.
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    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
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    Redmine #111. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
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    Redmine #111. Forgot to close italics.
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    Redmine #111. 5. Updated 2 links that were being redirected.
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    Redmine #111. Moved period out of hyperlink for Weiss track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
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    1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
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    1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
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    added a space in front of (PSU) for PSU TFBS and PSU Histone since they have the same description page.
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    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.
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    Redmine #110. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
• src/hg/makeDb/trackDb/rat/rn4/polyASeqSites.html
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    trackDb for polyA-Seq for rat
• src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
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    checking in Fan's branch for the rgdGene2 update
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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    checking in rgdGene2 search specs
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    trackDb for polyA-Seq for rat
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    trying to resolve conflict
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    one last bit of catch up for rgdGene2 checkin
• src/hg/makeDb/trackDb/rhesus/rheMac2/polyASeqSites.html
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    Added trackDb to polyASeq for Rhesus
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
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    Added trackDb to polyASeq for Rhesus
• src/hg/makeDb/trackDb/tagTypes.tab
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    adding bigBed to certain trackDb tags for the new bisulfite track
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    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
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    Initial descriptions for sarHar1.
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/gap.html
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    Initial descriptions for sarHar1.
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/gold.html
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    Initial descriptions for sarHar1.
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
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    Initial descriptions for sarHar1.
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
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    checking in Fan's branch for the rgdGene2 update
• src/hg/near/hgNear/hgNearData/Rat/rn4/genome.ra
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    checking in Fan's branch for the rgdGene2 update
• src/hg/near/hgNear/hgNearData/Rat/rn4/orderDb.ra
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    checking in Fan's branch for the rgdGene2 update
• src/hg/utils/automation/Encode.pm
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    bigBed loading ability added in
• src/hg/utils/automation/makeGenomeDb.pl
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    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
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    Polish the help message on ncbiAssemblyName and ncbiAssemblyId
• src/lib/bwgQuery.c
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    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
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    v263 preview2
• src/utils/qa/weeklybld/doNewBranch.csh
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    Tweaked the email checkin summary notice as per Ann's request
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    Chin is chinhli
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    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
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    Tweaked the email checkin summary notice as per Ann's request
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    Ann wanted me to check in the code to send a 'code summary reminder' to all persons who checked in code in this period.

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