#!/bin/sh

export LD_LIBRARY_PATH=/usr/local/apps/jellyfish-2.2.3/lib
KMER=21
THREADS=20

BASE=${1%%.*}
echo "File name base: $BASE"

echo "Running jellyfish..."
jellyfish count -s 1G -m ${KMER} -t ${THREADS} -o kmer -C $1
jellyfish dump -c -t kmer > ${BASE}.kmer${KMER}.txt

echo "Preparing histogram..."
awk '{print $2}' ${BASE}.kmer${KMER}.txt | sort -n | uniq -c | awk '{print $2 "," $1}' > ${BASE}.jf.hist