USeq Source Code

* 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

----USeq_8.9.4----
SamAlignmentExtractor
* Rewrote the app to enable processing deep coverage datasets without exceeding memory requirements. Added lots of QC metrics.
BamBlaster
* New app for injecting snv and indel variants from a vcf file into a bam file
BamMixer
* New app for mixing BamBlaster alignments into different frequency tumor samples
VCFMutationMaker
* New app to generate vcf files with random snvs and indels over target regions for BamBlaster