.TH FASTQ-MATCH 1

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

.SH SYNOPSIS
.B fastq-match [OPTION]... QUERY [FILE]...

.SH DESCRIPTION
Given a nucleotide sequence QUERY, perform local alignment against every FASTQ
sequence using the Smith-Waterman algorithm. For each read, an alignment score
is printed, so that the output consists of a simple list of scores.

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

.SH OPTIONS
.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>