USeq Source Code

Relaxed the thresholds for calling splice damaging/ creating variants.

Brought the RNASeq, ChIPSeq, and MultipleReplicaScanSeqs up to speed with DESeq2

Switched the default behavior to merge stranded datasets. These plus minus useq files were causing all kinds of grief.

Cleaned up the code in the VCFComparator. Put in some more catches for NA and INF vals coming back from R

Lots of clean up.
Updated DRDS to DESeq2: major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.

AlignmentEndTrimmer: This application can be used to trim alignments according to the density of mismatches. Each base of the alignment is compared to the reference sequence from the start of the alignment to the end. If the bases match, the score is increased by -m. If the bases don't match, the score is decreased by -n. The alignment position with the highest score is used as the new alignment end point. The cigar string, alignment position, mpos and flags are all updated to reflect trimming.

IntersectRegions: Added GC matching functionality. Didn't appear to be implemented in original version
RandomRegions: Did not return null if a region couldn't be found, which caused crashes.

Added enhancements to the diff splice detection utilities in DRDS including a graph output for diff spliced genes showing the per exon relative log2Rto. Having problems with DEXSeq and a high false positive rate.

IntersectRegions: Added support for interval trees
DRDSAnnotator: Added support for multiple rows of annotation for the same gene. Unique entries are concentated and reported.
IntervalTree: Added IntervalTree classes w/ Nix's edits. Added option to search for 'containing' regions intead of intersecting regions

BisStat
* Added fix for single stranded lambda datasets, these were crashing the app when calculating the non-conversion rate.
AllelicMethylationDetector
* Added fix for single stranded datasets, this was tossing chromosomes of data that didn't have both a plus and minus strand.
VCFComparator
* Added a catch for GQ scores that are floats instead of ints, was causing app to crash.