#! /bin/bash
VERSION=1.0.3
PREFIX=$1
FASTQ=$2

# If no user input, print usage
if [[ $# == 0 ]]; then
    echo "bactopia-sketcher - v${VERSION}"
    echo ""
    echo "bactopia-sketcher <PREFIX> <FASTQ> <OPT1> ... <OPTN>"
    echo ""
    exit
fi

if [[ "$1" == "version" ]] || [[ "$1" == "--version" ]]; then
    echo "bactopia-sketcher ${VERSION}"
    exit
fi

gzip -cd ${FASTQ} | mash sketch -o ${PREFIX}-k21 -k 21 -s 21 -r -I ${PREFIX} -
gzip -cd ${FASTQ} | mash sketch -o ${PREFIX}-k31 -k 31 -s 31 -r -I ${PREFIX} -
sourmash sketch dna -p k=21,k=31,k=51,abund,scaled=1000 --merge ${PREFIX} -o ${PREFIX}.sig ${FASTQ}
