USeq Source Code

edu.utah.tomato: lots of fixes and improvements
edu.utah.seq.vcf: Added automatic vcf chunking to improve memory usage
edu.utah.diagnostics: Metrics are now reported as html and can be merged. Fixed figures.
edu.utah.seq.data: Fixed error in CalculatePerCycleErrorRate. Only encountered when the number of phiX sequences is huge.

Added back in apps that we're compiling to the build props.

RNAEditingScanSeqs
* Added a minimum base fraction edited option to app to restrict what base observations are allowed into the analysis.
RNAEditingPileUpParser
* Fixed a bug where the parser was counting all of the reference reads (both plus and minus) when scoring a base for editing instead of just reads mapping to the matched strand when a stranded parsing was selected.

Added an option to reset the maximum alignment score, needed for parsing Evan Johnson's gnumap alignments.

Fixed error that broke ant script

First TomatoFarmer check-in.

Lots of mods related to adding edgeR functionality into Defined Region Diff Seq

Added ability to work on a directory of files

New apps imported from Picard and modified for extracting intenstiy info from CIF files

updated sam and picard jars