Generate alignments in SAM format given paired end reads using Maq.
bam alignment output file
BFA Index name
bfq files - forward files
bfq files - reverse files
fastq input files directory - reverse files
maq map output files
disable Smith-Waterman alignment
Any extra parameters
length of the first read (<=127)s
match in the colorspace
max distance between two paired reads s
max distance between two RF paired reads s
maximum allowed sum of qualities of mismatches
max number of hits to output. >512 for all 01 hits.
number of mismatches in the first 24bp
rate of difference between reads and references
length of the second read (<=127)s
trim all reads (usually not recommended)