-f

--fn-fasta

FILE

[ no default ]

FASTAreference file

-r

--fn-reads

FILE

Standardinput (stdin)

The reads file name

-i

--reads-format

STRING

Unknown

The reads file format(fastq | fq | fasta | fa |sam | bam)

-s

---fn-sam

FILE

Standardoutput (stdout)

The SAM file name

--bam-start-vfo

INT

0

Sets the starting virtual file offsets that limit the range of BAM reads to process

-A

--score-match

INT

1

Score for a match

-M

--pen-mismatch

INT

3

Mismatch penalty

-O

--pen-gap-open

INT

5

Indel start penalty

-E

--pen-gap-extension

INT

2

Indel extension penalty

-G

--pen-gap-long

INT

-1

Long indelpenalty