USeq Source Code

Lots of mods, see the release notes for 8.8.9.

1. TF metrics: Won't crash when processing bam files without phiX
2. VCFAnnotator: Fixed typos in logs and menu

Updated release notes for 8.8.9 release.

AllelicExpressionDetector - cleaned up code
SamAlignmentExtractor - removed option on printing coverage stats, now directing to a file instead of stdout
MultiSampleVCFFilter - fixed issue with gzipped vcfs and not tabix provided
SomaticSniperVCFParser - new app for inserting quality score into QUAL field and option for score filtering
VCFComparator - more mods to support bed file key variants

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.