Author:         Martin Asser Hansen - Copyright (C) - All rights reserved

Contact:        mail@maasha.dk

Date:           April 2008

License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)

Description:    Read Solexa deep sequenceing output files. Lowercase sequence indicates low quality.

Usage:          $script [options] -i <Solexa file(s)>

Options:   [-i <file(s)> | --data_in=<file(s)>]  -  Comma separated list of files or glob expression to read.
Options:   [-n <int>     | --num=<int>]          -  Limit number of records to read.
Options:   [-q <int>     | --quality=<int>]      -  Lowercase nucleotide with quality score below this limit (min:0 max:40)  -  Default=20
Options:   [-I <file>    | --stream_in=<file>]   -  Read input stream from file                                              -  Default=STDIN
Options:   [-O <file>    | --stream_out=<file>]  -  Write output stream to file                                              -  Default=STDOUT

Examples:   $script -i test.solexa             -  Read Solexa entries from file.
Examples:   $script -i test1.fna,test2.solexa  -  Read Solexa entries from files.
Examples:   $script -i '*.solexa'              -  Read Solexa entries from files.
Examples:   $script -i test.solexa -n 10       -  Read first 10 Solexa entries from file.
Examples:   $script -i test.solexa -q 10       -  Change quality score threshold to 10.

Keys out: SEQ_NAME    -  Name of sequence.
Keys out: SEQ         -  Sequence.
Keys out: SEQ_LEN     -  Length of sequence.
Keys out: SCORE_MEAN  -  Mean quality score.