Generate alignments in SAM format given paired end reads
fastq input files directory - reverse
output_bam
type: mapsource: fq_forward_inputcategory: outputoptional: {}pattern: ./*.bam
sai input files - forward
sai input files - reverse files
bwa database to align against
disable insert size estimate (force -s)
disable Smith-Waterman for the unmapped mate
maximum hits to output for paired reads
maximum insert size
maximum occurrences for one end
maximum hits to output for discordant pairs
preload index into memory (for base-space reads only)
prior of chimeric rate (lower bound)