DESCRIPTION

Unknown option: h usage: ./randomFQ (-c <count> | -p <pct>) [-fasta] [-out <prefix>] [-seed <int>] <input-fastq> [<input-2> [<index-3>] ]

Returns <count> number of random entries from the input fastq.

Output is fastq, unless you specify -fasta

If the -out parameter ends in .gz, the result is gzipped in-place.

-p returns a % of total reads, -c returns a fixed count.

SINGLE END:

Outputs to standard output, unless -out <file> is specified.

PAIRED END:

Pass 2 (or 3) files as input, -out is required.

If the paired-end output contains a "%" sign, it is replaced with the 1 & 2 for paired-end.

IE: -o output_%.fastq.gz

Otherwise it's jsut output_1 and output_2

*** If one file is an indexed read, it has to be the 3rd file (for now).