Global options used by all TMAP modules

-f

--fn-fasta

File

[ no default ]

FASTA reference 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

none

Integer

0

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

-A

--score-match

Integer

1

Score for a match.

-M

--pen-mismatch

Integer

3

Mismatch penalty.

-O

--pen-gap-open

Integer

5

INDEL start penalty.

-E

--pen-gap-extension

Integer

2

INDEL extension penalty.

-G

--pen-gap-long

Integer

-1

Long INDEL penalty.