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
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corrected an error in morgan's modification
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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
- lines changed 1, context: html, text, full: html, text
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
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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
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fixup color problem for chain net caePb3 tracks on ce10
- src/hg/hgc/hgc.c
- lines changed 2, 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/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
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Changed link from hard to relative
- src/hg/htdocs/ENCODE/dataSummary.html
- lines changed 2, context: html, text, full: html, text
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.
- lines changed 2, context: html, text, full: html, text
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
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Fixed table format and added link to FAQ
- 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
- lines changed 2, context: html, text, full: html, text
Changed example link to point to genome.ucsc.edu instead of genome-test.cse.ucsc.edu
- lines changed 2, context: html, text, full: html, text
Added db=hg19 to example URL
- src/hg/htdocs/goldenPath/newsarch.html
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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
- 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
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running a 7-way alignment to eliminate the two broken genomes
- lines changed 53, context: html, text, full: html, text
adding frames creation to the 7-way
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV9.release1.notes
- 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
- src/hg/makeDb/doc/hetGla1.txt
- src/hg/makeDb/doc/macEug2.txt
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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
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indicate which assemblies are updated in v65
- src/hg/makeDb/genbank/etc/align.dbs
- 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
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- 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 1, context: html, text, full: html, text
adding gorilla to the xrg definition
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adding ce10 and related nematodes
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 20, context: html, text, full: html, text
Registering new antibodies
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Expanding vendor abbreviation
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Updating PanIslet source description
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Adding PROVISIONAL status
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moved comments out of lines with var val pairs
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fixed regex to be more stringent
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fixed some interferon descriptions, uncovered problems
- lines changed 54, context: html, text, full: html, text
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
- 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
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 21, context: html, text, full: html, text
restored missing stanza from public
- 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 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 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 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.
- lines changed 1267, context: html, text, full: html, text
re-removed clusters from fresh file
- 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
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
- 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
- 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
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
- lines changed 4562, context: html, text, full: html, text
rename to new convention
- lines changed 4, context: html, text, full: html, text
changed html tag, and collapsed cd20 cell lines into one
- 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.
- lines changed 26, context: html, text, full: html, text
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.
- lines changed 1, context: html, text, full: html, text
Modified order of Inputs appearing in the matrix. Redmine #110, #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 29, context: html, text, full: html, text
Updated input meta-data. Redmine #110.
- lines changed 1, context: html, text, full: html, text
Modified order of Inputs appearing in the matrix. Redmine #110, #111.
- src/hg/makeDb/trackDb/t2g.html
- lines changed 7, context: html, text, full: html, text
corrections to t2g desc page
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 103, context: html, text, full: html, text
adding tracks chainNetFr3 chainNetOreNil1 cons7way chainNetCaePb3 chainNetCaeSp111 chainNetCaeRem4 chainNetCb4 chainNetCaeJap4 chainNetCaeAng1
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
prevExonText correction for t2g
- src/hg/makeDb/trackDb/wallaby/macEug2/description.html
- lines changed 53, context: html, text, full: html, text
final touch up for Wallaby
- lines changed 2, context: html, text, full: html, text
Final touch up of thml files
- src/hg/makeDb/trackDb/wallaby/macEug2/gap.html
- lines changed 42, context: html, text, full: html, text
Final touch up of thml files
- src/hg/makeDb/trackDb/wallaby/macEug2/gold.html
- lines changed 8, context: html, text, full: html, text
Final touch up of thml files
- src/hg/makeDb/trackDb/wallaby/macEug2/trackDb.ra
- lines changed 2, context: html, text, full: html, text
final touch up for Wallaby
- src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
- lines changed 107, context: html, text, full: html, text
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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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
- 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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