USeq Source Code

OK:
1) updating the .project file and the new way Eclipse creates faceted projects. Hopefully this minimize the hell of getting USeq installed in Eclipse
2) Added some mods to the CollectBamStats app to skip particular parsing if the log file doesn't have it
3) Added Z-Score calcs, graphs, and xls and bed output to PoReCNV to help in calling real CNVs

Made a number of changes as I'm writing the read pair flattener for barcoded reads.

Read lengths are calculated using the reported sequence vs perfect cigar. This avoids crashes when there are very few reads.

Added functionality to PoReCNV to join adjacent passing exons into larger CNV block.

Fixed an issue with PoReCNV where the last chromosome of data wasn't being processed when batching R calls.

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.