Torrent Browser User Interface Guide

TMAP Global Options

This page describes global TMAP options.

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

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

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