USeq Source Code

1. reset serverURL for createAnalysisMain to bioserver. It isn't working with Apache Tomcat.
2. changed code to require config file with run parameters

Autoaligner
1. Fix regexs to more explicitly match versioned genome, build code, and both paired-end fastq files
2. Modified build code and versioned genome to set as lower case to match case of approved index names
3. Fixed a bug that would print an error to log (saying dir wasn't created) when a new analysis report directory was created
4. Updated server URL for createAnalysisMain to hci-bio-app
5. Fixed logging errors
6. Added more new sequencing application codes
7. Logs now report how each sample is handled
Sample
1. added getters/setters for a number of new booleans

Initial commit of DRDSAnnotator

MicrosatelliteCounter: Added new options and will now skip reads with unterminated repeats

Added latest apps.

Latest mods for associating variants with splice junctions.

Added new MicrosatelliteCounter application.
Made small changes to the BisSeqAggregatePlotter and Gr2Bar apps.

Added an option to first call Picard's SortSam and MarkDuplicates

Wrapper for Picard's MarkDuplicates

Mods to STP to output just spliced alignments.
Mods to VCFAnnotator to convert scores to pvalues.
Mods to MiRNACorrelator to improve ggplot scripts.