Crate fasten_randomize

Create random reads from stdin.

Examples

print "hello world\n";

General usage

General usage to randomize the order of the reads

cat file.fastq | fasten_randomize > random.fastq

One read

Get one random read. Entries will always be in a 4-line format.

cat file.fastq | fasten_randomize | head -n 4 > one_read.fastq

Paired end

If paired, keep them together

cat R1.fastq R2.fastq | fasten_shuffle | fasten_randomize --paired-end | head -n 8 > one_pair.fastq

Usage

Usage: fasten_randomize [-h] [-n INT] [-p] [-v]
 
Options:
    -h, --help          Print this help menu.
    -n, --numcpus INT   Number of CPUs (default: 1)
    -p, --paired-end    The input reads are interleaved paired-end
    -v, --verbose       Print more status messages

Functions

• main 🔒
• print_reads_from_stdin 🔒
  Read fastq from stdin, add the reads to a vector, then print them to stdout in random order