USeq Source Code

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.

Mods to catch null data issues where no vcf records make it through the parsing. This was causing the app to crash out.

VCFSpliceAnnotator
* Bug fix for vcf output where vcf records with no changes were being truncated
SamSVFilter
* Mods for unsoft masking alignments for IGB visualization

ParsePointDataContexts: Fixed bug that would prematurely terminate PPDC if position 7206193 was encountered

MergeExonMetrics: Samples are now sorted in alphabetical order
MotifScanner: Motif hit orientation is now reported.

RNAEditingPileUpParser: Added option chrM, skips processing chrM

Added new app PullMatchingAlignments.
MotifScanner now reports the motif locations in the read.

Adding zscore support to the VCFSpliceAnnotator

SamTranscriptomeParser & DefinedRegionDifferentialSeq
* Replaced the IH tag with NH tag for reporting the number of alignments present per read to be compatible with DEXSeq's HTSeq app.

SamReadDepthSubSampler
* New app for reducing extreme read depths in amplicon based sequencing datasets

More mods to the SpliceJunction annotator for zscore estimations