USeq Source Code

All TF commands now report available diskspace in the stdout.txt file.

Sam2USeq: Prepend chr to bed regions, if it isn't there already.
TomatoFarmer: TomatoFarmer now injects a script into each cmd.txt file that determines the memory, cpus and GCThread count. Before the resources were set to the specs of the weakest nodes in our clusters. The commands also now report the the node that ran the job, which should help with future debugging.
VCFAnnotator: Added CADD scores, improved the genotype reporting in the last set of columns. VCFAnnotator should now work with FreeBayes output.

Dropped support for unsorted sam.gz files, this was causing issues with files that had no phiX

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.