Modified code to work with standard Illumina read names, rather than the fastq files output from fastq_to_table.
Skips fastq_to_table step.
Fixed variable errors vis-a-vis use strict
Re-implemented requirement that start/start positions are unique.
adding support for samtools rocksort
Added commands for samtools rocksort
fixed typos
Removed die now that the assignment seems to work
Attempting to make the samtools rocksort commands work a little more fluidly
Removed process reporting
checks for curl vs wget now.  Silly OS X....
Further changes re: not renaming reads
more wget/curl changes
fixed typo
Added check for R
Fixed error in substitution command
Added more checks for required programs
Starting to make changes so that chromos don't need renaming
UCI HPC-specific test file
changed perl path