All File Changes

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 2, context: html, text, full: html, text
    changed calculation method to round at the end
  • lines changed 34, context: html, text, full: html, text
    changed handling of attic objects, and also objects that changed states between old and new for tables and gbdbs
• python/lib/ucscgenomics/qa.py
  • lines changed 3, context: html, text, full: html, text
    made it 0 or more spaces before labels
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 1, context: html, text, full: html, text
    added mismatch penalty to encourage contiguous segments of alignment more
• src/ai/wordChain/wordChain.c
  • lines changed 16, context: html, text, full: html, text
    Debugging nonsense output.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 22, context: html, text, full: html, text
    Updating the dafs to what we are using now
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updating the dafs to what we are using now
• src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf
  • lines changed 41, context: html, text, full: html, text
    Added cv items for new repli-seq data from Gilbert lab. Also took the first stab at a DAF for the Human data set. Redmine #6627, #6626.
  • lines changed 1, context: html, text, full: html, text
    Fixed example DDF entry. Redmine #6626.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf
  • lines changed 20, context: html, text, full: html, text
    The TssHmm will now be displayed
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf
  • lines changed 1, context: html, text, full: html, text
    Updated bam validation to be 99.0%. Redmine #5697.
  • lines changed 1, context: html, text, full: html, text
    Forgot to increment the DAF version to 1.4 in previous commit: f84df47051abb23f950f4583df4dffaaa983edf7.
  • lines changed 4, context: html, text, full: html, text
    Updated daf to use 98% bam pass rate and require replicates being tracked for Signal and Peak views. Redmine #5697.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf
  • lines changed 20, context: html, text, full: html, text
    Proposed Changes to Take new file types and protocol
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed DAF for bedRnaElements to have sql table reference for loading purposes. Redmine #5986.
  • lines changed 2, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
  • lines changed 3, context: html, text, full: html, text
    quick fix for parsing error, but there are otehr problem with the script, max and I will go over
  • lines changed 2, context: html, text, full: html, text
    fixed a big where spaces in teh antibody name would name it to the validation document's filename
  • lines changed 4, context: html, text, full: html, text
    changed it to die on spaces in term name
  • lines changed 1, context: html, text, full: html, text
    made error more descriptive
• src/hg/encode/antibodyWikiParser/makefile
  • lines changed 16, context: html, text, full: html, text
    updated makefile for anitbody parser wiki
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 6, context: html, text, full: html, text
    fixing error messages for bigBed loader to say bigBed
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 9, context: html, text, full: html, text
    changed it to no filter on wgEncode
  • lines changed 2, context: html, text, full: html, text
    added exception for README.txt (it never shows up in the index)
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    fixed a big that had the initDate broken
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 5, context: html, text, full: html, text
    one part didn't ignore comments
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 6, context: html, text, full: html, text
    wrong test unmbering
• src/hg/hgGene/rgdInfo.c
  • lines changed 1, context: html, text, full: html, text
    fixup UniGene cluster ID to remove Rn. from the name redmine 29
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    Changed absolute links to relative.
• src/hg/hgTables/bedList.c
  • lines changed 5, context: html, text, full: html, text
    use fullTrackList global to fix huge memory over-consumption that occurred when doing a subtrack merge (#1114)
• src/hg/hgTables/seqOut.c
  • lines changed 6, context: html, text, full: html, text
    handle case in doGenomicDna where we were not printing the NO_RESULTS message (see #6873)
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Text change suggested by Greg, see redmine #5850
  • lines changed 3, context: html, text, full: html, text
    Ouch. Fixed problem created by uncareful use of {} brackets. Fallout from redmine 6622 checkin.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    hDbExists is not the function to use to see if a Db exists, that is only for hgcentral
• src/hg/hgTracks/searchTracks.c
  • lines changed 43, context: html, text, full: html, text
    revert previous commit; it turns out when need trackDb for first page in order to populate the group list (see #6931)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 19, context: html, text, full: html, text
    patches to t2g to make it work even if no article/sequence table exist
  • lines changed 42, context: html, text, full: html, text
    first go on marker display
  • lines changed 32, context: html, text, full: html, text
    first working version of t2gMarkerSnippets
• src/hg/hgc/gencodeClick.c
  • lines changed 31, context: html, text, full: html, text
    Fixed various GENCODE hgc layout problems RM: 6872
• src/hg/hgc/t2g.c
  • lines changed 16, context: html, text, full: html, text
    patches to t2g to make it work even if no article/sequence table exist
  • lines changed 22, context: html, text, full: html, text
    first go on marker display
  • lines changed 27, context: html, text, full: html, text
    first working version of t2gMarkerSnippets
  • lines changed 1, context: html, text, full: html, text
    trackDb changes for t2g
  • lines changed 12, context: html, text, full: html, text
    typo in track desc
  • lines changed 130, context: html, text, full: html, text
    sectioning selectors added
  • lines changed 13, context: html, text, full: html, text
    changed trackDb names in t2g.c.
  • lines changed 1, context: html, text, full: html, text
    removing an accidental debug instruction
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Adding PSU TFBS to the downloads page, redmine# 110
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Add update date
  • lines changed 1, context: html, text, full: html, text
    Add a year to update!
  • lines changed 139, context: html, text, full: html, text
    fixing the new Buske pub date info, removing instances of .. and adding a . after journal titles since most were missing
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 1, context: html, text, full: html, text
    I was wrong. It is called fetchChromSizes (not getChromSizes).
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 2, context: html, text, full: html, text
    I was wrong. It is called fetchChromSizes (not getChromSizes).
• src/hg/htdocs/goldenPath/help/cutters.html
  • lines changed 3, context: html, text, full: html, text
    Added 'Data last updated' per redmine #5850. Added Display header for clarity. Removed a couple extraneous p tags.
  • lines changed 38, context: html, text, full: html, text
    Reformated table html for easier reading/editing and axed the deprecated <font> tags in favor of css. Added a background-color to the table header row for better user experience.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 7, context: html, text, full: html, text
    Added pub from braney.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 7, context: html, text, full: html, text
    Fixed various GENCODE hgc layout problems RM: 6872
• src/hg/inc/trackDb.h
  • lines changed 3, context: html, text, full: html, text
    add trackDbAddSetting
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v263
• src/hg/js/hgTracks.js
  • lines changed 10, context: html, text, full: html, text
    Ajax reload of a track needs to update the tr's classes. This fixes 6329.
• src/hg/js/subCfg.js
  • lines changed 10, context: html, text, full: html, text
    Katrina is not happy that making one subtrack visible will turn on the set.
  • lines changed 4, context: html, text, full: html, text
    Andy Pohl tripped over a debug message when naming subtracks as {compisteName}_{subtrack}. This is easily fixed and should not be illegal. The debug message did what it was supposed to do.
• src/hg/lib/customFactory.c
  • lines changed 81, context: html, text, full: html, text
    remove CHECK_BAM_BIG_CHROM_SIZES code; will add backin if/when we decide to proceed with #2572
• src/hg/lib/ensFace.c
  • lines changed 1, context: html, text, full: html, text
    hDbExists is only for assembly databases to see if they are in dbDb, to see if a database exists, use sqlDatabaseExists
• src/hg/lib/hVarSubst.c
  • lines changed 8, context: html, text, full: html, text
    take out linkToGatewayPage variable. It's not necessary as using $db works
• src/hg/lib/trackDbCustom.c
  • lines changed 6, context: html, text, full: html, text
    add trackDbAddSetting
• src/hg/logCrawl/encodeUserDbCrawl/encodeUserDbCrawl.c
  • lines changed 204, context: html, text, full: html, text
    Adding a log-crawler that is fairly ENCODE specific.
• src/hg/logCrawl/encodeUserDbCrawl/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding a log-crawler that is fairly ENCODE specific.
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 86, context: html, text, full: html, text
    Finished bosTau7 genscan track
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release2.notes
  • lines changed 2511, context: html, text, full: html, text
    Added release 2 notes for track. Redmine #4145.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release1.notes
  • lines changed 196, context: html, text, full: html, text
    Standard Naming
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release2.notes
  • lines changed 871, context: html, text, full: html, text
    Cleaned up attic labels to fix the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release1.notes
  • lines changed 196, context: html, text, full: html, text
    Standard Naming
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes
  • lines changed 925, context: html, text, full: html, text
    Cleaned up attic labels to fix the notes file
  • lines changed 7, context: html, text, full: html, text
    Adding the V2 Contigs to the notes file and the mdb
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibRnaSeq.release1.notes
  • lines changed 85, context: html, text, full: html, text
    fixed notes for haib rna seq
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes
  • lines changed 31, context: html, text, full: html, text
    wgEncodeOpenChromSynth.release2.notes
  • lines changed 20, context: html, text, full: html, text
    updated notes again, gz md5sum bug rears it's ugly head
  • lines changed 15, context: html, text, full: html, text
    forgot to removed held back experiment
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release3.notes
  • lines changed 585, context: html, text, full: html, text
    added in notes for release 3 uw dgf
• src/hg/makeDb/doc/fr3.txt
  • lines changed 84, context: html, text, full: html, text
    starting on 8-way multiz
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 4, context: html, text, full: html, text
    document upstreamGeneTbl choice
• src/hg/makeDb/doc/hg19.txt
  • lines changed 64, context: html, text, full: html, text
    added two subtracks to ISCA composite
  • lines changed 1, context: html, text, full: html, text
    forgot to add date to DONE comment
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 2, context: html, text, full: html, text
    indicate windowmaskerSdust feature bits result
• src/hg/makeDb/doc/mm10.txt
  • lines changed 260, context: html, text, full: html, text
    getting ready to start genbank
  • lines changed 204, context: html, text, full: html, text
    genbank, cpgIslandExt, microsat, blatservers, default position done, running genscan
  • lines changed 94, context: html, text, full: html, text
    genscan done, featureBits complete, and in the pushQ
• src/hg/makeDb/doc/mm9.txt
  • lines changed 20, context: html, text, full: html, text
    done with mm9 to mm10 liftOver
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 3, context: html, text, full: html, text
    Putting in a few more tables to drop from the temp database before integration.
  • lines changed 59, context: html, text, full: html, text
    Fixing minor merge conflict.
  • lines changed 4, context: html, text, full: html, text
    Added a comment to rebuild the swissprot and proteins databases before starting the UCSC Genes script
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added mm10.
  • lines changed 1, context: html, text, full: html, text
    Added sarHar1 - Tasmanian devil
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 20, context: html, text, full: html, text
    adding mm10 definitions
  • lines changed 1, context: html, text, full: html, text
    set mm10.align.unplacedChroms = chr* since any of them can lift with the nonBridgedGap.lift file
  • lines changed 1, context: html, text, full: html, text
    incorrect spelling of mm10.nonBrided.lift file
  • lines changed 23, context: html, text, full: html, text
    Added sarHar1
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added mm10.
  • lines changed 1, context: html, text, full: html, text
    Added sarHar1 - Tasmanian devil
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding sarHar1 Tasmanian Devil
• src/hg/makeDb/schema/all.joiner
  • lines changed 23, context: html, text, full: html, text
    adding mm10 to the rules
  • lines changed 2, context: html, text, full: html, text
    Cleaned up a few rules relating to the tRNAs track and the connection between the tRNAs and kgXref. This would not have been possible without the wise perspective of Brooke. Brooke is a goddess...
• src/hg/makeDb/trackDb/README
  • lines changed 2, context: html, text, full: html, text
    add linkToGatewayPage
  • lines changed 2, context: html, text, full: html, text
    take out linkToGateway. Can be built with just $db
  • lines changed 2, context: html, text, full: html, text
    adding alwaysZero to supported tags in wig and bedGraph
• src/hg/makeDb/trackDb/anopheles/anoGam1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/armadillo/dasNov1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cat/felCat3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/chimp/panTro1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/chimp/panTro3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cow/bosTau2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Minor cv edits
  • lines changed 54, context: html, text, full: html, text
    added descriptions of validation docs + other fixes according to issue #6883
  • lines changed 7, context: html, text, full: html, text
    Adding terms for Proteogenomics protocols
  • lines changed 267, context: html, text, full: html, text
    Adding new antibodies
  • lines changed 3, context: html, text, full: html, text
    Fixing a bug in cv
  • lines changed 2, context: html, text, full: html, text
    Fixing MAZ bug
  • lines changed 70, context: html, text, full: html, text
    Added cv items for new repli-seq data from Gilbert lab. Also took the first stab at a DAF for the Human data set. Redmine #6627, #6626.
  • lines changed 75, context: html, text, full: html, text
    Added control specific terms for the eGFP antibodies. Redmine #5697.
  • lines changed 8, context: html, text, full: html, text
    Fixing antibody HMGB1
  • lines changed 11, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
  • lines changed 3, context: html, text, full: html, text
    Changing antibodies to fit naming convention
  • lines changed 311, context: html, text, full: html, text
    added new antibodies
  • lines changed 20, context: html, text, full: html, text
    Fixing ScienCell web links
  • lines changed 86, context: html, text, full: html, text
    Standardizing GeneCard Reg
  • lines changed 86, context: html, text, full: html, text
    Standardizing GeneCard References
  • lines changed 2, context: html, text, full: html, text
    Fixing TransFrags Description
  • lines changed 1, context: html, text, full: html, text
    Annotating HMEC as normal mammary cells
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1214, context: html, text, full: html, text
    Moving alpha cv to beta
  • lines changed 164, context: html, text, full: html, text
    Updating beta CV with alpha
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/dm1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/dm3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/dp2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/dp3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droAna1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droAna2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droEre1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droGri1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droMoj1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droMoj2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droPer1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droSec1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droSim1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droVir1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droVir2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droYak1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/drosophila/droYak2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/elephant/loxAfr1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/fugu/fr1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/fugu/fr2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 17, context: html, text, full: html, text
    update image include and assembly description
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/horse/equCab1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/horse/equCab2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/human/hg16/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 30, context: html, text, full: html, text
    Closed several list and paragraph html tags. Thanks, Greg.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1141, context: html, text, full: html, text
    Added in metadata and objects that were removed using old revoke policy to follow new revoke policy. Also updated md5sums. Redmine #4145, note #26.
  • lines changed 227, context: html, text, full: html, text
    Updated fileName to have .bai file and added md5sums. Redmine #4145.
  • lines changed 577, context: html, text, full: html, text
    Added expId's and accessioned experiments new for release 2. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 406, context: html, text, full: html, text
    Added protocol TAP-Only and found the missing subId 4061 data, see ticket 1634
  • lines changed 818, context: html, text, full: html, text
    This was part of the name change to Tap, I am not sure how it didn't get checked in
  • lines changed 1427, context: html, text, full: html, text
    Adding the Tap protocol to yet more object names
  • lines changed 9, context: html, text, full: html, text
    Clean up BJ Rep 1 rename issue
  • lines changed 872, context: html, text, full: html, text
    Fixing the ExonV7 files to have Tap in the name
  • lines changed 5, context: html, text, full: html, text
    Finding the missing files from 4468 submission
  • lines changed 267, context: html, text, full: html, text
    Resubmit of Contigs as Tap with no floats in the score field
  • lines changed 1432, context: html, text, full: html, text
    md5sums
  • lines changed 9, context: html, text, full: html, text
    Adding DCC accessions
  • lines changed 4, context: html, text, full: html, text
    Cleaned up attic labels to fix the notes file
  • lines changed 11, context: html, text, full: html, text
    Changing the 2 H1-hesc contigs files to have V2 and have -1 instead of .
  • lines changed 3, context: html, text, full: html, text
    Adding the V2 Contigs to the notes file and the mdb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 4, context: html, text, full: html, text
    Name change to add Tap protocol into the names
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 246, context: html, text, full: html, text
    added in last missing tracks
  • lines changed 16, context: html, text, full: html, text
    revoked objects and added md5sums
  • lines changed 5, context: html, text, full: html, text
    missed some revoked, put in now
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 1796, context: html, text, full: html, text
    added in a lot of new tracks to open chrom dnase,a dn amde release 2 html
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 773, context: html, text, full: html, text
    Added in full set of files for track from submission 5451. Redmine #225
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 46, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
  • lines changed 1, context: html, text, full: html, text
    Removing protocol as a expID
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.obsolete.ra
  • lines changed 40, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.ra
  • lines changed 40, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 241, context: html, text, full: html, text
    added in expIds and accessions for UwDgf
  • lines changed 110, context: html, text, full: html, text
    added origAssembly=hg19 to new objects
  • lines changed 1, context: html, text, full: html, text
    Removed origAssembly line from wgEncodeUwDgf section
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging UW Repli-seq on beta, redmine 4577
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 17351, context: html, text, full: html, text
    staging HAIB TFBS (Release 2), redmine# 4487
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 2948, context: html, text, full: html, text
    Staging UW DNaseI DGF on beta, redmine #5406
  • lines changed 109, context: html, text, full: html, text
    Re-staging metadata on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwRepliSeq.ra
  • lines changed 7955, context: html, text, full: html, text
    staging UW Repli-seq on beta, redmine 4577
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromSynth.ra
  • lines changed 227, context: html, text, full: html, text
    Releasing Open Chrom Synth (Release 2) to RR (redmine #5405)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 3112, context: html, text, full: html, text
    Releasing UW DNaseI DGF (Release 3) to the RR (redmine #5406)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    added two subtracks to ISCA composite
  • lines changed 2, context: html, text, full: html, text
    added two subtracks to ISCA composite. added release alpha to html override
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
  • lines changed 1, context: html, text, full: html, text
    adding trackDb include for release 3 dgf
  • lines changed 1, context: html, text, full: html, text
    staging UW Repli-seq on beta, redmine 4577
  • lines changed 2, context: html, text, full: html, text
    staging HAIB TFBS (Release 2), redmine# 4487
  • lines changed 3, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
  • lines changed 2, context: html, text, full: html, text
    Staging UW DNaseI DGF on beta, redmine #5406
  • lines changed 1, context: html, text, full: html, text
    moving openChromDNase to release2 tag
  • lines changed 2, context: html, text, full: html, text
    Releasing Open Chrom Synth (Release 2) to RR (redmine #5405)
  • lines changed 2, context: html, text, full: html, text
    Releasing UW DNaseI DGF (Release 3) to the RR (redmine #5406)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 12, context: html, text, full: html, text
    Updated Release notes for track. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
  • lines changed 180, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 4206, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
  • lines changed 4, context: html, text, full: html, text
    Changing hard links to relative links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Changing hard links to relative links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 1, context: html, text, full: html, text
    Changing hard links to relative links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
  • lines changed 90, context: html, text, full: html, text
    Cleaning out old comments mostly, a few more changes according to ticket 1634
  • lines changed 9, context: html, text, full: html, text
    html changes according to preQA ticket http://redmine.soe.ucsc.edu/issues/1634#note-96
  • lines changed 3, context: html, text, full: html, text
    Changing hard links to relative links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra
  • lines changed 375, context: html, text, full: html, text
    Added protocol TAP-Only and found the missing subId 4061 data, see ticket 1634
  • lines changed 116, context: html, text, full: html, text
    Name change to add Tap protocol into the names
  • lines changed 2, context: html, text, full: html, text
    Commented out color and type lines for wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalMinusRawRep1 which seem to be comming from subId 4061. The lines were breaking the make. Redmine #1634.
  • lines changed 2, context: html, text, full: html, text
    removed duplicate tags that broke make
  • lines changed 11, context: html, text, full: html, text
    merge fix
  • lines changed 186, context: html, text, full: html, text
    Adding the Tap protocol to yet more object names
  • lines changed 6, context: html, text, full: html, text
    Clean up BJ Rep 1 rename issue
  • lines changed 1, context: html, text, full: html, text
    Finding the missing files from 4468 submission
  • lines changed 26, context: html, text, full: html, text
    Resubmit of Contigs as Tap with no floats in the score field
  • lines changed 169, context: html, text, full: html, text
    Fixed labels and made tags not start with numerals
  • lines changed 5, context: html, text, full: html, text
    Changing the 2 H1-hesc contigs files to have V2 and have -1 instead of .
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 25, context: html, text, full: html, text
    revising wording, redmine #6230
  • lines changed 149, context: html, text, full: html, text
    Restructured the paragraphs
  • lines changed 46, context: html, text, full: html, text
    Fixing merge conflict, this will likely need more review, the merge went very badly
  • lines changed 57, context: html, text, full: html, text
    Trying to fix issues in the ticket for Katrina, this is a work in progress that I am checking in for her to put on beta
  • lines changed 21, context: html, text, full: html, text
    Changing the Display Section to match other encode tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 13, context: html, text, full: html, text
    Trying to fix issues in the ticket for Katrina, this is a work in progress that I am checking in for her to put on beta
  • lines changed 19, context: html, text, full: html, text
    Still trying to resolve color with Katrina
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 103, context: html, text, full: html, text
    added in last missing tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    removed extraneous letters
  • lines changed 397, context: html, text, full: html, text
    fixed short labels at labs request
  • lines changed 8, context: html, text, full: html, text
    forgot to fix the too long ones
  • lines changed 4, context: html, text, full: html, text
    lab preferred changes to the too long ones
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
  • lines changed 0, context: html, text, full: html, text
    added a missing space
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 1492, context: html, text, full: html, text
    moving openChromDNase to release2 tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
  • lines changed 310, context: html, text, full: html, text
    added in a lot of new tracks to open chrom dnase,a dn amde release 2 html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 1492, context: html, text, full: html, text
    moving openChromDNase to release2 tag
  • lines changed 361, context: html, text, full: html, text
    added in a lot of new tracks to open chrom dnase,a dn amde release 2 html
  • lines changed 33, context: html, text, full: html, text
    Added in treatment subGroups for track that were missing in commit: 840a873d9180863c4a6a015cf33d8b8c52b50a10. Redmine #4143.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 88, context: html, text, full: html, text
    qa fixes for synth html
  • lines changed 5, context: html, text, full: html, text
    fixed references
  • lines changed 1, context: html, text, full: html, text
    fixed release date
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 16, context: html, text, full: html, text
    homogenized short labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegNorm.ra
  • lines changed 2, context: html, text, full: html, text
    Updating a couple more places from 7 to 9 cell lines.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
  • lines changed 3, context: html, text, full: html, text
    wgEncodeRikenCage.release3.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 55, context: html, text, full: html, text
    Added in full set of files for track from submission 5451. Redmine #225
  • lines changed 1, context: html, text, full: html, text
    Updated the scoreFilter to be default 0. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 108, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
  • lines changed 174, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
  • lines changed 1, context: html, text, full: html, text
    Changing hard links to relative links
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 110, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
  • lines changed 0, context: html, text, full: html, text
    Fixed errant tabs according to code review
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html
  • lines changed 175, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra
  • lines changed 32, context: html, text, full: html, text
    Merging UncBsuProt and UncBsuProtFasp into UncBsuProt.release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
  • lines changed 166, context: html, text, full: html, text
    renaming .new to release3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 1568, context: html, text, full: html, text
    renaming .new to release3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.html
  • lines changed 166, context: html, text, full: html, text
    renaming .new to release3
  • lines changed 30, context: html, text, full: html, text
    qa fixes for uwDgf redmine 5406
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra
  • lines changed 1568, context: html, text, full: html, text
    renaming .new to release3
  • lines changed 147, context: html, text, full: html, text
    short and long labels
  • lines changed 4, context: html, text, full: html, text
    fixed some straggling labels
  • lines changed 3, context: html, text, full: html, text
    fixed visibility settings
  • lines changed 9, context: html, text, full: html, text
    fixed defaults, and set max display mode to full
  • lines changed 1, context: html, text, full: html, text
    set max display mode back to dense
  • lines changed 1, context: html, text, full: html, text
    changed html over to release tag
  • lines changed 80, context: html, text, full: html, text
    removing accession tags
  • lines changed 12, context: html, text, full: html, text
    qa fixes for uwDgf redmine 5406
  • lines changed 4, context: html, text, full: html, text
    fixed defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
  • lines changed 14, context: html, text, full: html, text
    Fixes for Redmine #4577 4. Replaced semicolon with comma between cell line and replicate 5. Replaced comma with semicolon before G1/G1b list in description section 6. Removed comma after G2 in description section 7 .Removed comma after Percetage-Normalized Signal in descrption section 8. Removed comma after Peaks in description section 9. Removed comma after Valleys in description section 10. Removed hyphen between weighted average 11. Italicized in vivo 12. Removed semicolons and made 3 seperate sentences in long section of first paragrah in methods section 13 Broke up long on going sentence in last paragraph of Methods section 15. Updated references to be to NCBI Pubmed. 16. Updated Long labels to be consitent and use Repli-seq instead of Replication Timing
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixes for Redmine #4577 1. Changed alphabetical order of HeLa-S3 and HepG2 2. Changed alphabetical order of BJ and BGO2ES
  • lines changed 32, context: html, text, full: html, text
    Fixes for Redmine #4577 4. Replaced semicolon with comma between cell line and replicate 5. Replaced comma with semicolon before G1/G1b list in description section 6. Removed comma after G2 in description section 7 .Removed comma after Percetage-Normalized Signal in descrption section 8. Removed comma after Peaks in description section 9. Removed comma after Valleys in description section 10. Removed hyphen between weighted average 11. Italicized in vivo 12. Removed semicolons and made 3 seperate sentences in long section of first paragrah in methods section 13 Broke up long on going sentence in last paragraph of Methods section 15. Updated references to be to NCBI Pubmed. 16. Updated Long labels to be consitent and use Repli-seq instead of Replication Timing
  • lines changed 1, context: html, text, full: html, text
    Fixed issues in Redmine #4577 18. Fixed spelling of header in hgFileUi for Phase from Hase
• src/hg/makeDb/trackDb/human/iscaComposite.alpha.html
  • lines changed 136, context: html, text, full: html, text
    added two subtracks to ISCA composite
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 1, context: html, text, full: html, text
    strengthened warning about using the data
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Starter trackDb for AffyCytoScan
  • lines changed 54, context: html, text, full: html, text
    added two subtracks to ISCA composite
• src/hg/makeDb/trackDb/lamprey/petMar1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/lizard/anoCar1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding mm10 to the build
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/max.larryPop.trackDb.ra
  • lines changed 106, context: html, text, full: html, text
    my own local trackDb files
• src/hg/makeDb/trackDb/max.pubDens.trackDb.ra
  • lines changed 252, context: html, text, full: html, text
    my own local trackDb files
• src/hg/makeDb/trackDb/max.trackDb.ra
  • lines changed 39, context: html, text, full: html, text
    my own local trackDb files
  • lines changed 29, context: html, text, full: html, text
    added some test tracks
  • lines changed 4, context: html, text, full: html, text
    changed trackDb stanza names
• src/hg/makeDb/trackDb/medaka/oryLat1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/medaka/oryLat2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/mouse/mm10/description.html
  • lines changed 132, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 95, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 55, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 17, context: html, text, full: html, text
    update description and gold and gap pages to better match reality
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/mouse/mm7/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/mouse/mm8/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/mouse/mm9/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 902, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 239, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 223, context: html, text, full: html, text
    add expId, dccAccession to entries with ages other than adult-8wks
  • lines changed 162, context: html, text, full: html, text
    try to fix failed merge
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 5, context: html, text, full: html, text
    Releasing PSU TFBS mm9, Redmine #110
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
  • lines changed 6542, context: html, text, full: html, text
    Releasing PSU TFBS mm9, Redmine #110
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    renaming wgEncodeLicrRnaSeq.new.ra to wgEncodeLicrRnaSeq.release2.ra, update trackDb.wgEncode.ra for this change
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    change wrangler from Venkat to Fang, renaming wgEncodeLicrHistone.new.ra to wgEncodeLicrHistone.release2.ra, update trackDb.wgEncode.ra for this change
  • lines changed 2, context: html, text, full: html, text
    change wrangler from Venkat to Fang, renaming wgEncodeLicrTfbs.new.ra to wgEncodeLicrTfbs.release2.ra, update trackDb.wgEncode.ra for this change
  • lines changed 1, context: html, text, full: html, text
    Releasing PSU TFBS mm9, Redmine #110
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.html
  • lines changed 146, context: html, text, full: html, text
    add Caltech desription page which is downloaded from redmine (Caltech_mouse_RNA-Seq_Track_Description_2011-09-01.html)
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    changed 'the precise' to 'their precise' in 'In general, these are associated with gene activity, but the precise relationships remain to be established.' which is a bit vague
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Removed incorrect 2 on long label.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 1, context: html, text, full: html, text
    Fixed hardcoded link to relative link. Redmin #6526.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
  • lines changed 162, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 27, context: html, text, full: html, text
    Forgot submittions 5439 in data load. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.new.ra
  • lines changed 56, context: html, text, full: html, text
    set vertical viewing range of H3K27ac to 0-5
  • lines changed 55, context: html, text, full: html, text
    had merge conflict in wgEncodeLicrHistone.new.ra, this is probably caused by last roll back where the viewLimits 0:5 of H3K27ac was added, now this is removed. Strangely this merge conflict message did not show up yesterday when roll back happened. Nothing has been done to this file today
  • lines changed 65, context: html, text, full: html, text
    re-add viewLimit 0:5 for H3K27ac after rollback
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    change wrangler from Venkat to Fang, renaming wgEncodeLicrHistone.new.ra to wgEncodeLicrHistone.release2.ra, update trackDb.wgEncode.ra for this change
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
  • lines changed 930, context: html, text, full: html, text
    change wrangler from Venkat to Fang, renaming wgEncodeLicrHistone.new.ra to wgEncodeLicrHistone.release2.ra, update trackDb.wgEncode.ra for this change
  • lines changed 150, context: html, text, full: html, text
    add age information to long label, modified short label to <=17 char long
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    remove strain from fileSorOrder as all the samples have the same strain
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    add age to sortOrder
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    remove #autogenerated comment
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    add empty GEO_accession column, Morgan will request GEO_accession in batch later
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.new.ra
  • lines changed 226, context: html, text, full: html, text
    add age to short and long labels and make cell line name more numan readable in long labels
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    changed Sig to Sg, Aln to Al, 8W to 8wk in some short labels
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    add age, GEO_Accession to fileSortOrder
  • lines changed 797, context: html, text, full: html, text
    renaming wgEncodeLicrRnaSeq.new.ra to wgEncodeLicrRnaSeq.release2.ra, update trackDb.wgEncode.ra for this change
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
  • lines changed 115, context: html, text, full: html, text
    added file wgEncodeLicrRnaSeq.release2.html which is a copy of wgEncodeLicrRnaSeq.html
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    In the Description paragraph, changed C57Bl/6 to C57BL/6added detailed mouse tissue, primary cell and their age group information.
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    added release note for release2
  • lines changed 1, context: html, text, full: html, text
    remove the space in the end of the release note
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    modified the release note to reflect the new experiments added since release 1
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    added the following notes to the Release Notes :\nThe row is changed to the subtrack list which is right below the configuration box in the Track Settings page.\nAge column is added to the subtrack list which is right below the configuration box in the Track Settings page.\nAge and GEO Accession columns are added to the downloadable file list in the Downloads page
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
  • lines changed 797, context: html, text, full: html, text
    renaming wgEncodeLicrRnaSeq.new.ra to wgEncodeLicrRnaSeq.release2.ra, update trackDb.wgEncode.ra for this change
  • lines changed 76, context: html, text, full: html, text
    re-add strain to long lable which probably got removed after roll back
  • lines changed 1, context: html, text, full: html, text
    turn off autoScale
  • lines changed 1, context: html, text, full: html, text
    added 'html wgEncodeLicrRnaSeq.release2' to the composite stanza (top stanza)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.new.ra
  • lines changed 702, context: html, text, full: html, text
    change wrangler from Venkat to Fang, renaming wgEncodeLicrTfbs.new.ra to wgEncodeLicrTfbs.release2.ra, update trackDb.wgEncode.ra for this change
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra
  • lines changed 702, context: html, text, full: html, text
    change wrangler from Venkat to Fang, renaming wgEncodeLicrTfbs.new.ra to wgEncodeLicrTfbs.release2.ra, update trackDb.wgEncode.ra for this change
  • lines changed 125, context: html, text, full: html, text
    modified shortLabel to have it's length<=17, add age information to long labels
  • lines changed 13, context: html, text, full: html, text
    remove #autogenerated comment
  • lines changed 2, context: html, text, full: html, text
    added age to sortOrder in tracking setting page; removed strain column from fileSortOrder in Downloads page as the experiments uses the same strain; added empty GEO_accession column to fileSortOrder in Downloads page, Morgan will request GEO_accession number in batch later
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 41, context: html, text, full: html, text
    Updated longLabels to fix inconsistency found in QA process. Redmine #110.
• src/hg/makeDb/trackDb/opossum/monDom1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/opossum/monDom4/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/other/nemVec1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/pig/susScr2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/rabbit/oryCun1/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/rat/rn3/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/rat/rn4/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/refGene.new.html
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    add new genbank trackDb.ra for doc changes for #6237
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 9, context: html, text, full: html, text
    added a bit of explanation to the listing of 4 SNP tracks
• src/hg/makeDb/trackDb/squirt/ci1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/squirt/ci2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/stickleback/gasAcu1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 1, context: html, text, full: html, text
    typo in track desc
• src/hg/makeDb/trackDb/tRNAs.html
  • lines changed 26, context: html, text, full: html, text
    Made a few adjustments to Credits and References sections
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    Add a line to explain why some tRNA images are rotated
  • lines changed 6, context: html, text, full: html, text
    Updated track decription with note about rotated images, per redmine #6921
• src/hg/makeDb/trackDb/tagTypes.tab
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    adding alwaysZero to supported tags in wig and bedGraph
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    sectioning selectors added
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    resolving git conflict
• src/hg/makeDb/trackDb/tetraodon/tetNig1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/tetraodon/tetNig2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
  • lines changed 220, context: html, text, full: html, text
    add new genbank trackDb.ra for doc changes for #6237
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 219, context: html, text, full: html, text
    extract genbank tracks to there own ra file (so release tagging is easier) #6237
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    jim s enhancers tests
  • lines changed 29, context: html, text, full: html, text
    resolved conflict in sandbox
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    sandbox additions: pub density tracks
  • lines changed 10, context: html, text, full: html, text
    trackDb changes for larry's pop track, sandbox only
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    added some test tracks
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    trackDb changes for t2g
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    Merge branch 'master' into maxDev2
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    small changes to track names
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    sectioning selectors added
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    extract genbank tracks to there own ra file (so release tagging is easier) #6237
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    add new genbank trackDb.ra for doc changes for #6237
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/urchin/strPur1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/wallaby/macEug1/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/caeJap1/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/caePb1/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/caePb2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/caeRem2/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/caeRem3/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/cb1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/cb3/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/ce10/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/ce2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/ce4/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/ce6/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/worm/priPac1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/xenTro/xenTro1/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/xenTro/xenTro2/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebrafish/danRer3/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebrafish/danRer4/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebrafish/danRer5/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
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    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
  • lines changed 3, context: html, text, full: html, text
    added a note about the Genbank assembly quality at the bottom. #6237
• src/hg/near/hgNear/hgNearData/Rat/rn4/genome.ra
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    fixup select statement for allTranscriptQuery
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
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    Fixing off by one score column for narrowPeak and adding some verbose status.
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    Fixing minor merge conflict.
• src/hg/txCds/txCdsPredict/txCdsPredict.c
  • lines changed 12, context: html, text, full: html, text
    Updating usage information to show actual output.
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    Fixing minor merge conflict.
• src/hg/utils/automation/HgDb.pm
  • lines changed 38, context: html, text, full: html, text
    added functionality to recursively walk back include statements for easier management of .hg.conf files
• src/hg/utils/genomeQuality/genomeQuality.pl
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    correct plural word
• src/isPcr/isPcr/isPcr.c
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    Finishing implementing minSize option.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    mention fetchChromSizes in these usage messages, redmine 6844
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    mention fetchChromSizes in these usage messages, redmine 6844
• src/utils/qa/weeklybld/buildEnv.csh
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    v263 final build
• src/utils/qa/weeklybld/makeZip.csh
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    Added handly README.txt to the zipped source at Maximilian Haeussler's request.
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 2, context: html, text, full: html, text
    mention fetchChromSizes in these usage messages, redmine 6844

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• files changed: 458