USeq Source Code

Added changes and apps to support BamQC for the H1K project.

DefinedRegionDifferentialSeq: Changed rLog to rlogTransformation. Apparently rLog is phased out in newer versions
TomatoFarmer: Fixed some constant names

Lots of mods related to splice site identification in VCF files, improvements to our bam file QC apps, and extended functionality for comparing VCF files with a relaxed key of BamSurgeon induced variants.

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.