USeq Source Code

Lots of mods to the individual VCF parsers to standardize them for merging with Somatic variant analysis.

More mods to the PoReCNV app.

Fixed an issue with the CollectBamStats where changes to the default thresholds were being overwritten.

Fixed an issue with the convertSangerQualityScores() method. Base recalibration is boosting the scores so need to not throw an error when encountering these values.

Finalized the normal exome CNV discovery app. Modified several VCF parsers to insert their app name into the ID field to assist with merging.

Added threading to the cnv app.

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.