useq Source Code changes

Just modified the bed file output to contain the read counts.

biotelerock — Wed, 30 Sep 2015 16:43:32 -0000

Just modified the bed file output to contain the read counts.
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Big refactoring of the molecular barcode consenus calling tools to utilize preprocesing with the FastqBarcodeTagger MatchMates followed by Consensus. This cut the time in 1/2 and memory requirements ...

biotelerock — Wed, 23 Sep 2015 20:58:23 -0000

Big refactoring of the molecular barcode consenus calling tools to utilize preprocesing with the FastqBarcodeTagger MatchMates followed by Consensus. This cut the time in 1/2 and memory requirements to < 30G. This is ready to go and stable.
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A bit of package rearrangements to accomidate the molecular barcode clustering and consensus classes.

biotelerock — Fri, 04 Sep 2015 23:08:51 -0000

A bit of package rearrangements to accomidate the molecular barcode clustering and consensus classes.
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Lots of mods and new apps. More tweaks to the json output from Sam2USeq. More options for outputing data from mpileup files. Fixes to VCF classes to work with DNANexus vcf calls on NIST datasets. Fin...

biotelerock — Wed, 05 Aug 2015 14:56:49 -0000

Lots of mods and new apps. More tweaks to the json output from Sam2USeq. More options for outputing data from mpileup files. Fixes to VCF classes to work with DNANexus vcf calls on NIST datasets. Finally fixed the java 1.8 compatibility issue with GenomicRegions. Lastly, new app for inserting barcodes from a third fastq file into paired fastq datasets.
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Added ability to parse multi sample mpileup files

biotelerock — Fri, 31 Jul 2015 21:10:41 -0000

Added ability to parse multi sample mpileup files
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Hmm, can't seem to upload a release to SF's Files?! Was failing Friday. Moving the site to GitHub......

biotelerock — Mon, 27 Jul 2015 15:39:46 -0000

Hmm, can't seem to upload a release to SF's Files?! Was failing Friday. Moving the site to GitHub......
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Sam2USeq

biotelerock — Mon, 27 Jul 2015 15:32:17 -0000

Sam2USeq * Added a failed bed region output for those target bases with less than the indicated depth. Good for identifying holes in particular locations, and deletions. Sam2USeq, CalculatePerCycleErrorRate, SamAlignmentExtractor, MergePairedAlignments * Added option to export key QC metrics in json format * Moved base summary stats to MergePairedAlignments to get a more accurate uniOb count for total, Q20, and Q30 MergeRegions * Fixed issue of running this on java 1.7+ with contract sort violation MpileupParser * New App for parsing a SAMTools mpileup output file for non reference bases generating PointData for the reference, non reference, and fraction non reference for bases that pass the minimum read coverage filter. Histogram * Changed counters to use long instead of int to avoid overflow, this affects ~10 apps
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Lots of mods related to filtering sam alignments for quality to deal with the NextSeq500 data. New features for the simulated tumor sample generation apps.

biotelerock — Fri, 10 Jul 2015 22:24:29 -0000

Lots of mods related to filtering sam alignments for quality to deal with the NextSeq500 data. New features for the simulated tumor sample generation apps.
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Made a variety of modifications to support a new app, BamMixer, that wraps a variety of useq apps to generate simulated somatic datasets. Adding in another new app, VCFVariantMaker that generates a v...

biotelerock — Fri, 26 Jun 2015 17:16:02 -0000

Made a variety of modifications to support a new app, BamMixer, that wraps a variety of useq apps to generate simulated somatic datasets. Adding in another new app, VCFVariantMaker that generates a vcf file of random snv and indels for use with the BamBlaster app.
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Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.

biotelerock — Fri, 19 Jun 2015 19:40:01 -0000

Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.
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