Use BWA to align a set of fastq reads against a db
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.sai
stop searching when there are >INT equally best hits
input sequences are in the color space
bwa database to align against
max
gap_ext_max
type: integerdefault: {}optional: True
gap extension penalty
gap open penalty
maximum number or fraction of gap opens
log-scaled gap penalty for long deletions
maximum occurrences for extending a long deletion
maximum entries in the queue
mismatch penalty
do not put an indel within INT bp towards the ends
non-iterative mode search for all n-difference hits (slow)
quality threshold for read trimming down to 35bp
Seed length
Maximum differences in the seed
number of threads