.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH DAMAPPER "1" "August 2020" "damapper" "User Commands"
.SH NAME
damapper \- long read to reference genome mapping tool
.SH DESCRIPTION
Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool.	
.SH SYNOPSIS
.B damapper
[\fI\,-vpzCN\/\fR] [\fI\,-k<int(20)>\/\fR] [\fI\,-t<int>\/\fR] [\fI\,-M<int>\/\fR] [\fI\,-T<int(4)>\/\fR] 
[\fI\,-P<dir(/tmp)>\/\fR] [\-e<double(.85)] [\-s<int(100)>] [\-n<double(1.00)>] [\-m<track>]+  
<reference:dam> <reads:db> ...
.HP
\fB\-k\fR: k\-mer size (must be <= 32).
.HP
\fB\-t\fR: Ignore k\-mers that occur >= \fB\-t\fR times in a block.
.HP
\fB\-M\fR: Use only \fB\-M\fR GB of memory by ignoring most frequent k\-mers.
.HP
\fB\-e\fR: Look for alignments with \fB\-e\fR percent similarity.
.HP
\fB\-s\fR: Use \fB\-s\fR as the trace point spacing for encoding alignments.
.HP
\fB\-n\fR: Output all matches within this % of the best
.HP
\fB\-T\fR: Use \fB\-T\fR threads.
.HP
\fB\-P\fR: Do sorts and merges in directory \fB\-P\fR.
.HP
\fB\-m\fR: Soft mask the blocks with the specified mask.
.HP
\fB\-v\fR: Verbose mode, output statistics as proceed.
.HP
\fB\-z\fR: sort .las by A,B\-read pairs (overlap piles)
.IP
off => sort .las by A\-read,A\-position pairs (default for mapping)
.HP
\fB\-p\fR: Output repeat profile track
.HP
\fB\-C\fR: Output reference vs reads .las.
.HP
\fB\-N\fR: Do not output reads vs reference .las.