SAM tools, bare bones implementation.

Can run sam to bam, sam index and sam sort.

input.infile_ = 
input.inf_bam_sort_ = (this is only available when sam_to_bam_ = 0) bam input for sorting
input.inf_bam_index_ = (this is only available when sam_to_bam_=0 and bam_sort_=0) bam input for sorting


vparam.runtime_ = (float) Maximum Hours to Run; default = 0.25, max 168
vparam.sam_to_bam_ = (switch) Run Sam to BAM analysis (requires SAM input), default=1
vparam.bam_sort_ = (switch) Run BAM sort (required BAM input); default=1
vparam.bam_index_ = (switch) Run BAM index; default=1