USeq Source Code

1. TomatoFarmer: bug fixes and improvements
2. VCFAnnotator: New annovar versions can be incorporated more easily.
3. MethylationArrayScanner: New option for T-Test
4. SamAlignment: the 'chr' is no longer added to chromosomes. This would cause STP to create two versions of the chromosomes in the header.
5. SamTranscriptomeParser: Relaxed @SQ line matching
6. DefinedRegionDifferentialSeq: Fixed SAMSeq error when there was more than two conditions. New option to turn off DESeq2 independent filtering

Lots of mods....

Adding app to cluster samples in a multi sample vcf file to validate the relationship structure or lack there of.

added polyA tag getter

Lots of mods:

MultiSampleVCFFilter
* Added option to filter by region
* Cleaned up chunking issues when no chunking is indicated
VarScanVCFParser
* New app to extract SOMATIC calls and replace QUAL score with the ssc score.
SamAlignmentExtractor
* Added option to output alignments that don't intersect the regions.
BamSurgeonMutator
* Generates random mutations in a list of regions for the BamSurgeon application
BisStat
* Fixed an issue where some runs were throwing a comparator contract sort error due to lack of data in a particular base context and thus null fraction values

Added option to filter vcfs by region, cleaned un chunking when no chunks called.

DRDS: Fixed a bug that would report zero counts for the last chromosome in the header when the bam file contains unmapped reads at the end of the file.

Added new app to randomly split sam files, mods to MergeSam to filter for bad BamSurgeon reads, removed catch in VCFSample that required read counts for observations (NIST GIB vcfs don't have these).

TomatoFarmer: Graph label changes and pipeline name changes.

Added new app for MergingSam files, a catch for alignments going off the end of chromosomes, updated docs.