aq-syntheticfastq.1

.\" Authors: Andre Masella
.TH aq-syntheticfastq 1 "October 2011" "1.2" "USER COMMANDS"
.SH NAME 
aq-syntheticfastq \- Apply real quality masks to arbitrary data
.SH SYNOPSIS
.B aq-syntheticfastq
[
.B \-j
] 
.B \-f 
.I file.fastq
.I sequence
.SH DESCRIPTION
For testing purposes, it is helpful to create arbitrary data with real quality masks. Given a sequence, a new FASTQ file is created by discarding the sequences from the original file and replacing them with the given sequence but preserving the quality mask.
.SH OPTIONS
.TP
\-f
The FASTQ file to be used for quality masks.
.TP
\-j
The input file is compressed with
.BR bzip (1).
.TP
sequence
The sequence to be used in the output. The output is as long as the shorter of the read or the input sequence.
.SH SEE ALSO
.BR axiome (1).