Add BWA 0.7.5a to dependencies
Add Cosmos dependency
Document creation of new BWA index (for the new MEM algorithm)
Add scripts for splitting and chunking FASTQ data
Add Picard MarkDuplicates dependency
Add script for generating Cosmos configuration
Skeleton Cosmos wrapper around the pipeline
Add alignment and PCR duplicate removal tools
Cosmos pipeline updates and bug fixes
New wrapper script for Sputnik that handles BAM inputs and produces BAM outputs
Support BAM subregions in wrap_sputnik.sh
Add samtools dependency
Add samtools and sputnik; no longer remove "chr" prefix from chromosomes--use EXACTLY what is in the sequence dict
Detect directory containing wrap_sputnik.sh to locate the sputnik binary
Don't prepend ./ to sputnik executable.  Full path is found by dirname
Add Sputnik and BAM indexing to workflow.  Increasing remdup time to 24h for long queue.  Let SortSam convert to BAM (by recognizing extension of the output file)
Index Sputnik's BAMs in preparation for MSItools
Simple R script for joining candidates by loci where genotypes exist across all samples
Let user specify list of chromosomes to analyze on the command line
Write supporting read records to stdout.  Move all diagnostic, runtime and debug messages to stderr.