Torrent Browser User Interface Guide


Torrent Suite Software space on Ion Community

User Interface Guide TOC

TMAP Global Options

This page describes global TMAP options.

Global options used by all TMAP modules

Option Alternate option Type Default Description

-f

--fn-fasta FILE

[ no default ]
FASTA reference file
-r

--fn-reads

FILE Standard

input (stdin)

The reads file name

-i --reads-format STRING Unknown

The reads file format

(fastq | fq | fasta | fa | sff | sam | bam)

-s ---fn-sam FILE Standard

output (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 indel penalty

Global flowspace options

Option Alternate option Type Default Description

INT

Global pairing options

Option Alternate option Type Default Description

-Q

--pairing INT 0

The insert pairing:

  • 0 Do not perform pairing
  • 1 Mate pairs (-S 0 -P 1)
  • 2 P aired end (-S 1 -P 0)

INT -1
INT -1
FLOAT -1.0
FLOAT -1.0