USeq Source Code

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

Minor mods to DRDS with option to exclude utr bps from analysis.

Lots of mods, most are related to changing a method for parsing bed files giving the option to ignore strand.