USeq Source Code

Added option to keep duplicate marked alignments. Now defaults to keeping them.

Fixed an issue with the JavaxComOrgInfoNetClasses.zip archive, needed to update this to contain the latest Excel POI classes. More mods for H1K BamQC. This is complete now and ready to go. Fixed an issue with the VarScanVCFParser where it wasn't inserting the ssc score into the QUAL field.

Fixed a bug that reported all Hugo names as NA

Fixed a major bug where variants were not being filtered against the commonly interrogated regions!

Fixed and issue with replacing the QUALity value with the ssc score from VarScan

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....