Crate fasten_mutate

Mutates reads. There is no mutation model; only randomness.

Examples

cat testdata/four_reads.fastq | fasten_mutate > out.fastq

Usage

 
Usage: fasten_mutate [-h] [-n INT] [-p] [-v] [-s INT] [-m]
 
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
    -s, --snps INT      Number of SNPs (point mutations) to include per read.
    -m, --mark          lowercase all reads but uppercase the SNPs (not yet
                        implemented)

Functions

main

mutate

Mutate a str of a sequence of nucleotides using the nucleotides in a vector nts. This function does not use any kind of mutation model and will choose random positions to replace with random nucleotides.