.TH FASTQ-GREP 1

.SH NAME
fastq-grep - print sequences matching a pattern

.SH SYNOPSIS
.B fastq-grep [OPTION]... PATTERN [FILE]...

.SH DESCRIPTION
Given a PATTERN, specified as a perl-compatible regular expression, print every
FASTQ entry with a matching nucleotide sequence.

One ore more FILEs may be specified, otherwise input is read from standard input.
Input files may be gziped.

.SH OPTIONS
.TP 
\fB\-i\fR, \fB\-\-id\fR
Match the read ID (by default, the sequence is matched).
.TP
\fB\-v\fR, \fB\-\-invert\-match\fR
Invert the sense of matching, to select non-matching entries.
.TP
\fB\-m\fR, \fB\-\-mismatches=FILE\fR
Output non-matching entries to the given file.
.TP
\fB\-c\fR, \fB\-\-count\fR
Suppress normal output; instead output the number of matching (or, non-matching,
with '-v') entries.
.TP
\fB\-h\fR, \fB\-\-help\fR
Output a help message and exit.
.TP
\fB\-V\fR, \fB\-\-version\fR
Output version information and exit.

.SH AUTHOR
Written by Daniel C. Jones <dcjones@cs.washington.edu>