USeq Source Code

Finished CalculatePerCyclePerNucleotideErrorRate. It would be useful to extend this to looking for insertion/deletion errors by position as well, instead of simply providing counts for the number of reads with insertion/deletion events.

Sam2USeq: Fixed an issue where chromData from the MergePairedAlignments app fail to calc read coverage with b37 no "chr" data. Now must match the bed file with the alignments.

PoReCNV: change the way loaded data is saved to enable per sample loading for additional runs.

VCF mods to support parsing of LoFreq's crazy vcf format

New app for converting a bed file to a gene table by intersecting it with another gene table.

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