All File Changes

v261_preview to v261_preview2 (2011-12-13 to 2011-12-20) v261

• python/lib/ucscgenomics/mkChangeNotes.py
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    modifications for morgan's new ra.py changes
• python/lib/ucscgenomics/ra.py
  • lines changed 5, context: html, text, full: html, text
    corrected an error in morgan's modification
  • lines changed 1, context: html, text, full: html, text
    error in making the common set of stanzas, not intersection of self and self, that's just plain wrong
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    corrected backward changes
• src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDfg.daf
  • lines changed 76, context: html, text, full: html, text
    Renamed Daf file to true composite name as Dgf instead of Dfg.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDgf.daf
  • lines changed 76, context: html, text, full: html, text
    Renamed Daf file to true composite name as Dgf instead of Dfg.
  • lines changed 9, context: html, text, full: html, text
    Updated to version 1.2 to have require replicate column.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
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    Checking in a stub for bigBed Validation
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
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    changed comparison to public vs alpha instead of beta vs alpha
• src/hg/hgCustom/hgCustom.c
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    Addendum to commit 1dd2ddbe9355 that angie made to include BAM and VCF in the list of formats that need to be embedded in a track line. The wording is in two places. I added a comma to one spot and the file formats in the other spot.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    show assembly next to scale bar (redmin #4073)
• src/hg/hgTracks/chromGraphTrack.c
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    pass id to imgTrackAddMapItem (fixes #6370)
• src/hg/hgTracks/hgTracks.c
  • lines changed 30, context: html, text, full: html, text
    show assembly next to scale bar (redmin #4073); add code to support pdf in hgRenderTracks (currently only live in larrym's tree)
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    make imgTrackAddMapItem tolerant of NULL id (fixes #6370)
• src/hg/hgTracks/netTrack.c
  • lines changed 3, context: html, text, full: html, text
    fixup color problem for chain net caePb3 tracks on ce10
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    incorporated larrym's changes to source code style
  • lines changed 1, context: html, text, full: html, text
    fixup color problem for chain net caePb3 tracks on ce10
• src/hg/hgc/hgc.c
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    MLQ #6291 (pgSNP format): the pgSnp lib function printSeqCodDisplaywas firing off a query to knownGene without first testing whether knownGene exists, causing error for knownGene-less databases. Now the lib function takes genePredTable as argument and tests existence before querying.
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    MLQ #6291: per Greg's request, updating pgSnp codon display tables to use<table class="descTbl"> instead of setting properties like borderwidth etc.
• src/hg/hgc/t2g.c
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    incorporated larrym's changes to source code style
• src/hg/hgc/vcfClick.c
  • lines changed 3, context: html, text, full: html, text
    MLQ #6291 (pgSNP format): the pgSnp lib function printSeqCodDisplaywas firing off a query to knownGene without first testing whether knownGene exists, causing error for knownGene-less databases. Now the lib function takes genePredTable as argument and tests existence before querying.
• src/hg/htdocs/ENCODE/contributors_pilot.html
  • lines changed 1, context: html, text, full: html, text
    Changed link from hard to relative
• src/hg/htdocs/ENCODE/dataSummary.html
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    Changed link from hard to relative
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 2, context: html, text, full: html, text
    Changed link from hard to relative
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 29, context: html, text, full: html, text
    Inserted script type declarations into HEAD. Inserted new euro class into links that need to be made relative.
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    Modified path to js directory
• src/hg/htdocs/ENCODE/index.html
  • lines changed 11, context: html, text, full: html, text
    Inserted script type declarations into HEAD. Inserted new euro class into links that need to be made relative.
• src/hg/htdocs/ENCODE/pilot.html
  • lines changed 1, context: html, text, full: html, text
    Changed link from hard to relative
• src/hg/htdocs/ENCODE/submission.html
  • lines changed 11, context: html, text, full: html, text
    Changed links from hard to relative
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 41, context: html, text, full: html, text
    Added FAQ about Error 500, Redmine #4401
  • lines changed 5, context: html, text, full: html, text
    Fixed table format and added link to FAQ
  • lines changed 1, context: html, text, full: html, text
    Fixed table format
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    Fixed table, last time
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 5, context: html, text, full: html, text
    Uncommented a reference to the VCF track format page
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 2, context: html, text, full: html, text
    Fixed a formatting problem in one of the examples
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    Made some minor formatting corrections
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 4, context: html, text, full: html, text
    Uncommented two references to the VCF track format page
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    Changed example link to point to genome.ucsc.edu instead of genome-test.cse.ucsc.edu
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    Added db=hg19 to example URL
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    Changed links from hard to relative
• src/hg/htdocs/images/euFlag.gif
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    modified EU flag to match US flag in size and enhanced stars a bit
• src/hg/htdocs/images/phylo/ce10_7way.png
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    7-way diagram for ce10 multiz
• src/hg/htdocs/indexNews.html
  • lines changed 19, context: html, text, full: html, text
    Added VCF announcement
• src/hg/htdocs/js/staticDoc.js
  • lines changed 6, context: html, text, full: html, text
    added code so users on the euronode will stay on the euronode url when they run into a genome hard link, redmine# 6368
• src/hg/htdocs/style/HGStyle.css
  • lines changed 3, context: html, text, full: html, text
    Added a class, .stdTbl, since this is really the style for displaying a standard table. Added a comment noting that we should really have one class here, not 3. But that's a to-do.
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    show assembly next to scale bar (redmin #4073)
• src/hg/inc/pgSnp.h
  • lines changed 1, context: html, text, full: html, text
    MLQ #6291 (pgSNP format): the pgSnp lib function printSeqCodDisplaywas firing off a query to knownGene without first testing whether knownGene exists, causing error for knownGene-less databases. Now the lib function takes genePredTable as argument and tests existence before querying.
• src/hg/js/hgTracks.js
  • lines changed 34, context: html, text, full: html, text
    more inPlaceUpdating (live only in larrym's tree)
• src/hg/lib/encode/bedRnaJunctions.as
  • lines changed 13, context: html, text, full: html, text
    First pass at creating a .as file that is structured for the Junctions data from caltech.
  • lines changed 1, context: html, text, full: html, text
    Updated schema to use -1 if no IDR is run.
• src/hg/lib/pgSnp.c
  • lines changed 10, context: html, text, full: html, text
    MLQ #6291 (pgSNP format): the pgSnp lib function printSeqCodDisplaywas firing off a query to knownGene without first testing whether knownGene exists, causing error for knownGene-less databases. Now the lib function takes genePredTable as argument and tests existence before querying.
  • lines changed 2, context: html, text, full: html, text
    MLQ #6291: per Greg's request, updating pgSnp codon display tables to use<table class="descTbl"> instead of setting properties like borderwidth etc.
• src/hg/lib/rgdGene2KeggPathway.as
  • lines changed 1, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/lib/rgdGene2ToKeggEntrez.as
  • lines changed 1, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/lib/rgdGene2ToSymbol.as
  • lines changed 1, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/lib/rgdGene2Xref.as
  • lines changed 1, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/lib/rgdGenePathway.as
  • lines changed 2, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/lib/rgdPathway.as
  • lines changed 2, context: html, text, full: html, text
    fixing mismatched quotes, spelling errors, field IDs that didn't match what was in the table due to spelling. For RGD Genes. Edits to Fan's changes here: http://redmine.soe.ucsc.edu/issues/29#note-143 and also to rgdGene2KeggPathway.as
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 856, context: html, text, full: html, text
    Initial work for bosTau7
• src/hg/makeDb/doc/ce10.txt
  • lines changed 833, context: html, text, full: html, text
    running a 7-way alignment to eliminate the two broken genomes
  • lines changed 12, context: html, text, full: html, text
    entering pushQ
  • lines changed 53, context: html, text, full: html, text
    adding frames creation to the 7-way
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV9.release1.notes
  • lines changed 70, context: html, text, full: html, text
    Adding notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibRnaSeq.release1.notes
  • lines changed 660, context: html, text, full: html, text
    Changing the names to drop out the ShortPolyA which was wrong, and adding in html bam information.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes
  • lines changed 128, context: html, text, full: html, text
    notes for release2 open chrom synth
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 418, context: html, text, full: html, text
    updated notes to reflect the restoring of revoked data
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    Removing Clusters
• src/hg/makeDb/doc/hetGla1.txt
  • lines changed 408, context: html, text, full: html, text
    genbank done
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 56, context: html, text, full: html, text
    Finished wallaby initial release.
• src/hg/makeDb/doc/makeEnsembl.txt
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    version 65 update done
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    version 65 update dateReference updated
  • lines changed 16, context: html, text, full: html, text
    indicate which assemblies are updated in v65
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hetGla1 - moleRat
• src/hg/makeDb/genbank/etc/blackList.txt
  • lines changed 7, context: html, text, full: html, text
    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 24, context: html, text, full: html, text
    Added hetGla1
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hetGla1 - moleRat
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 4, context: html, text, full: html, text
    adding hetGla1 moleRat
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • lines changed 17, context: html, text, full: html, text
    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/makeDb/genbank/src/process/gbProcessStep
  • lines changed 12, context: html, text, full: html, text
    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Add macEug2
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    adding gorilla to the xrg definition
  • lines changed 1, context: html, text, full: html, text
    Add macEug2 to
  • lines changed 17, context: html, text, full: html, text
    adding ce10 and related nematodes
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 14, context: html, text, full: html, text
    Code Review fixes
  • lines changed 20, context: html, text, full: html, text
    Registering new antibodies
  • lines changed 2, context: html, text, full: html, text
    Expanding vendor abbreviation
  • lines changed 5, context: html, text, full: html, text
    Updating PanIslet source description
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    Adding PROVISIONAL status
  • lines changed 18, context: html, text, full: html, text
    moved comments out of lines with var val pairs
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    fixed regex to be more stringent
  • lines changed 5, context: html, text, full: html, text
    fixed some interferon descriptions, uncovered problems
  • lines changed 12, context: html, text, full: html, text
    Added 2 new ages.
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    Added 3 new Mouse cell/Tissue registrations.
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    forgot to escape the plus last time
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 62, context: html, text, full: html, text
    Moving alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 410, context: html, text, full: html, text
    Moved changes that are good, and omitted any tag's with PROVISIONAL in the description. Changes are part of the normal cv Maven process: Redmine #6306 In addition changes move over Human and Mouse validation tags that link to the following tickets: Redmine #1012 #6055
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 4, context: html, text, full: html, text
    Use Human Mutation article as reference for geneReviews track.
  • lines changed 2, context: html, text, full: html, text
    Corrected citation format
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    removed extra space
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    added month to citation
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 21, context: html, text, full: html, text
    restored missing stanza from public
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    added md5sums
  • lines changed 1048, context: html, text, full: html, text
    Removing the GencCode V3
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 29, context: html, text, full: html, text
    fixed some metadata issues, added expIds and accessions
  • lines changed 2, context: html, text, full: html, text
    added md5sum
  • lines changed 5, context: html, text, full: html, text
    fixed some metadata issues caused by reloads
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 460, context: html, text, full: html, text
    Changing the names to drop out the ShortPolyA which was wrong, and adding in html bam information.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 9, context: html, text, full: html, text
    added in treatment=None values
  • lines changed 17, context: html, text, full: html, text
    removed unnecessary origAessembly lines
  • lines changed 21, context: html, text, full: html, text
    added dcc accessions to synth
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 3586, context: html, text, full: html, text
    restored missing metaData form public
  • lines changed 152, context: html, text, full: html, text
    added revoke tags to all the restored metadata
  • lines changed 134, context: html, text, full: html, text
    added md5sums
  • lines changed 714, context: html, text, full: html, text
    removed stanzas from public that have no files left also added in dccaccessions and expids where possible
  • lines changed 13, context: html, text, full: html, text
    added bais
  • lines changed 6, context: html, text, full: html, text
    fleshed out replaced message
  • lines changed 74, context: html, text, full: html, text
    cleaned up the restored stanzas, there were many errors
  • lines changed 1340, context: html, text, full: html, text
    Removing the clusters again, we are getting new ones
  • lines changed 1340, context: html, text, full: html, text
    Revert "Removing the clusters again, we are getting new ones" This reverts commit 09d9948a9918c35ecb5ffe6ba9b2cdd4a12853e6.
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    re-removed clusters from fresh file
  • lines changed 14, context: html, text, full: html, text
    Adding md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1837, context: html, text, full: html, text
    metadata for batch job
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 11, context: html, text, full: html, text
    filled in the rest of the dccAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 40, context: html, text, full: html, text
    rebuilt the beta.mdb.ra for cshl short's metaData update
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 5445, context: html, text, full: html, text
    remade the beta.mdb.ra for riken for dccaccession push
  • lines changed 369, context: html, text, full: html, text
    restaging the beta mdb for Riken
  • lines changed 11431, context: html, text, full: html, text
    Fixing merge conflicts
  • lines changed 74, context: html, text, full: html, text
    staging metadata on beta, #2020
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 1106, context: html, text, full: html, text
    staging UW Affy Exon release2, redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 931, context: html, text, full: html, text
    releasing dccAccession numbers, redmine #6067
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    pushing a patch for HAIB TFBS out to the RR, redmine# 6917
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 132, context: html, text, full: html, text
    releasing dccAccessions, #6067
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Change references in snp135 tracks (x4) to panTro3, as per the make doc, it seems that was intended.
  • lines changed 5, context: html, text, full: html, text
    Remove the hg18 liftOver flag from SIB tracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    renamed openchromchip with release tag
  • lines changed 1, context: html, text, full: html, text
    changed over to release conventions for synth
  • lines changed 2, context: html, text, full: html, text
    pushing a patch for HAIB TFBS out to the RR, redmine# 6917
  • lines changed 2, context: html, text, full: html, text
    fixed in trackDb
  • lines changed 2, context: html, text, full: html, text
    staging UW Affy Exon release2, redmine# 5314
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
  • lines changed 207, context: html, text, full: html, text
    adding John Kim's new description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 5, context: html, text, full: html, text
    added release 2 notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 112, context: html, text, full: html, text
    added obtained by to the subgroups becuase we have colliding objects without it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 4, context: html, text, full: html, text
    Changing the names to drop out the ShortPolyA which was wrong, and adding in html bam information.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 166, context: html, text, full: html, text
    Changing the names to drop out the ShortPolyA which was wrong, and adding in html bam information.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.html
  • lines changed 94, context: html, text, full: html, text
    Removing release 2, combined into release 1
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.ra
  • lines changed 1212, context: html, text, full: html, text
    Removing release 2, combined into release 1
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 84, context: html, text, full: html, text
    pushing a patch for HAIB TFBS out to the RR, redmine# 6917
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 1112, context: html, text, full: html, text
    renamed openchromchip with release tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
  • lines changed 315, context: html, text, full: html, text
    added in html for open chrom release 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 1112, context: html, text, full: html, text
    renamed openchromchip with release tag
  • lines changed 10, context: html, text, full: html, text
    moved progfibro to be near the other fibroblasts
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.new.ra
  • lines changed 196, context: html, text, full: html, text
    changed over to release conventions for synth
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 294, context: html, text, full: html, text
    added in html for synth release 2
  • lines changed 17, context: html, text, full: html, text
    open chrom synth release 2 fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 196, context: html, text, full: html, text
    changed over to release conventions for synth
  • lines changed 35, context: html, text, full: html, text
    pre-qa changes for synth
  • lines changed 11, context: html, text, full: html, text
    open chrom synth release 2 fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 131, context: html, text, full: html, text
    moved html over
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 648, context: html, text, full: html, text
    batch loaded submissions
  • lines changed 4562, context: html, text, full: html, text
    rename to new convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html
  • lines changed 131, context: html, text, full: html, text
    moved html over
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
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    rename to new convention
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    changed html tag, and collapsed cd20 cell lines into one
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    changed long labels
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 1009, context: html, text, full: html, text
    Added Inputs for track. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 162, context: html, text, full: html, text
    Updated input meta-data. Redmine #110.
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    Removed extraneous alignment file for track. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 58, context: html, text, full: html, text
    Added Inputs for track. Redmine #111.
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    Modified order of Inputs appearing in the matrix. Redmine #110, #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
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    Updated input meta-data. Redmine #110.
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    Modified order of Inputs appearing in the matrix. Redmine #110, #111.
• src/hg/makeDb/trackDb/t2g.html
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    corrections to t2g desc page
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
• src/hg/makeDb/trackDb/trackDb.ra
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    prevExonText correction for t2g
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
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    final touch up for Wallaby
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    Final touch up of thml files
• src/hg/makeDb/trackDb/wallaby/macEug2/gap.html
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    Final touch up of thml files
• src/hg/makeDb/trackDb/wallaby/macEug2/gold.html
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    Final touch up of thml files
• src/hg/makeDb/trackDb/wallaby/macEug2/trackDb.ra
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    final touch up for Wallaby
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
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    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
• src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
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    adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
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    fixup errors in the type chain specifications
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    adding entry for ce10 chain net
• src/hg/near/hgMapToGene/hgMapToGene.c
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    Resolving Redmine # 6093. The knownToRefSeq and knownToEnsembl tables contained cases where a small noncoding gene was overlapping a coding gene, often in the intron. To fix this, I did two things. First, I fixed a bug whereby if two candidate matches had the same score, the match to the shorter sequence was taken - even if both candidate matches had a score of zero. This generated a lot of false matches. Second, after discussing the situation with Jim, I added a requirement that as well as sharing some exonic bases, the two sequences must share a splice site unless they're both unspliced. This further decreases spurious matches between short ncRNAs and long coding genes
• src/hg/pslCDnaFilter/algo.txt
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    oops.. update the doc too! #6312
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/pslCDnaFilter/cDnaStats.c
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/pslCDnaFilter/cDnaStats.h
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/pslCDnaFilter/pslCDnaFilter.c
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    fix a stupid mistake I made in the decay min coverage function. Thanks Angie #6312
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    change a comment that isn't useful, into one that actually describes what is being done. Per Jim.
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/pslCDnaFilter/usage.txt
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    oops.. update the doc too! #6312
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/hg/utils/automation/EnsGeneAutomate.pm
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    adding v65 definitions
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    there is a new panTro4 for v65
• src/hg/utils/automation/doEnsGeneUpdate.pl
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    eliminate wget warning: timestamping does nothing in combination with -O. See the manual
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    update to Ensembl peptide fasta header syntax parsing
• src/hg/utils/genomeQuality/genomeQuality.pl
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    initial source
• src/inc/blackList.h
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/inc/common.mk
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    Updating local default version of samtools to 0.1.18.
• src/lib/blackList.c
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/lib/makefile
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    implement black list for genbank pipeline and pslCDnaFilter part of #20
• src/utils/qa/weeklybld/buildEnv.csh
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    v261 preview2

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