Activity for USeq
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David Nix created a blog post
USeq has moved to GitHub
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Just modified the bed file output to contain th...
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USeq released /USeq_8.9.6.zip
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Big refactoring of the molecular barcode consen...
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A bit of package rearrangements to accomidate t...
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Lots of mods and new apps. More tweaks to the j...
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Added ability to parse multi sample mpileup files
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Hmm, can't seem to upload a release to SF's Fil...
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Sam2USeq
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Lots of mods related to filtering sam alignment...
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Made a variety of modifications to support a ne...
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Whole lot of mods and apps related to Bam QC, E...
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Daniel Baker committed [r298]
Finished CalculatePerCyclePerNucleotideErrorRat...
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Sam2USeq: Fixed an issue where chromData from t...
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OK:
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Made a number of changes as I'm writing the rea...
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Timothy Mosbruger committed [r294]
Read lengths are calculated using the reported ...
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Added functionality to PoReCNV to join adjacent...
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Fixed an issue with PoReCNV where the last chro...
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All TF commands now report available diskspace ...
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Sam2USeq: Prepend chr to bed regions, if it isn...
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Dropped support for unsorted sam.gz files, this...
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Lots of mods to the individual VCF parsers to s...
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Fixed an issue with the convertSangerQualitySco...
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Finalized the normal exome CNV discovery app. M...
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Added threading to the cnv app.
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Lots of mods, see the release notes for 8.8.9.
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1 committed [r283]
1. TF metrics: Won't crash when processing bam ...
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Updated release notes for 8.8.9 release.
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AllelicExpressionDetector - cleaned up code
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Added option to keep duplicate marked alignment...
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Fixed an issue with the JavaxComOrgInfoNetClass...
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Fixed a bug that reported all Hugo names as NA
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Fixed a major bug where variants were not being...
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Fixed and issue with replacing the QUALity valu...
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Added changes and apps to support BamQC for the...
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DefinedRegionDifferentialSeq: Changed rLog to r...
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Lots of mods related to splice site identificat...
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1. TomatoFarmer: bug fixes and improvements
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Lots of mods....
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Adding app to cluster samples in a multi sample...
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ChristianP committed [r269]
added polyA tag getter
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Lots of mods:
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Added option to filter vcfs by region, cleaned ...
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DRDS: Fixed a bug that would report zero counts...
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Added new app to randomly split sam files, mods...
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TomatoFarmer: Graph label changes and pipeline ...
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Added new app for MergingSam files, a catch for...
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TomatoFarmer:
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Lots of clean up of the documentation and addit...
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SamTranscriptomeParser: @RG and @PG lines canno...
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Added lates changes to releaseNotes.txt
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Lots of mods to Telescriptor and related classe...
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1. STP bug fix
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Latest release notes
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Adding in changes for Misc and Num.
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1. TomatoFarmer updates
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Lots of modifications to the Telescriptor app
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Telescriptor changes.
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More static methods....
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Fixed a warning message related to exon size, a...
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Mods to support the Telescriptor....
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New app and supporting classes for detailed Tel...
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Added more output options for showing sample na...
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Modified default bps to extract alignment count...
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Added option to skip alt comparison when scorin...
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AlignmentEndTrimmer
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AllelicExpressionDetector
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AlignmentEndTrimmer: Option -s added to drop re...
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Darren Ames committed [r241]
Added some new classes, updates to Autoaligner ...
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Deleted TF straggler
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TomatoFarmer Overhaul
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Updated picard jars. They did a big package rea...
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Modified RNASeq app to use DESeq2 for the scann...
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Relaxed the thresholds for calling splice damag...
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Brought the RNASeq, ChIPSeq, and MultipleReplic...
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Switched the default behavior to merge stranded...
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Cleaned up the code in the VCFComparator. Put ...
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Lots of clean up.
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AlignmentEndTrimmer: This application can be us...
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IntersectRegions: Added GC matching functionali...
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