.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ_FILTER "1" "October 2014" "Fastaq" "Fastaq executables"
.SH NAME
fastaq_filter
.SH DESCRIPTION
 fastaq_filter [options] <infile> <outfile>
.PP
Filters a fasta/q file by sequence length and/or by name matching a regular
expression
.SS "positional arguments:"
.TP
infile
Name of fasta/q file to be filtered
.TP
outfile
Name of output fasta/q file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-min_length\fR INT
Minimum length of sequence to keep [0]
.TP
\fB\-\-max_length\fR INT
Maximum length of sequence to keep [inf]
.TP
\fB\-\-regex\fR REGEX
If given, only reads with a name matching the regular
expression will be kept
.TP
\fB\-\-ids_file\fR IDS_FILE
If given, only reads whose ID is in th given file will
be used. One ID per line of file.
.TP
\fB\-v\fR, \fB\-\-invert\fR
Keep sequences that do not match the filters


.SH "AUTHOR"
.sp
fastaq_filter was originally written by Martin Hunt (mh12@sanger.ac.uk)

.SH "COPYING"
.sp
Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&.