runOEA.sh

#!/bin/bash

# Author: Ehsan Haghshenas (ehaghshe[at]sfu[dot]ca)

if [ "$#" -lt 5 ]; then
   echo "USAGE: ./runOEA.sh pacbio.fasta illumina.fastq outDirectory outPrefix threads"
   exit
fi

EXEDIR=$(dirname "${BASH_SOURCE[0]}")
CURRDIR=`pwd`
LRFILE=$(readlink -e "${1}")
SRFILE=$(readlink -e "${2}")
OUTDIR=$(readlink -f "${3}")
OUTPRE=$(basename "${4}")
NTHREAD=$5
BWAOPTIONS="-aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5 -t $NTHREAD"

BWA=${EXEDIR}/bin/bwa-proovread
SAM=${EXEDIR}/bin/samtools
SPALG=${EXEDIR}/bin/spCorrection
OEAALG=${EXEDIR}/bin/oeaCorrection

CORR=${OUTDIR}/${OUTPRE}_corr
OEA=${OUTDIR}/${OUTPRE}_oea

mkdir -p ${OUTDIR}
# rm -f ${OUTDIR}/*
ln -s -f ${LRFILE} ${CORR}.fasta

${BWA} index ${CORR}.fasta
${BWA} mem ${BWAOPTIONS} ${CORR}.fasta ${SRFILE} > ${OEA}.sam
rm ${CORR}.fasta.amb ${CORR}.fasta.ann ${CORR}.fasta.bwt ${CORR}.fasta.pac ${CORR}.fasta.sa
${SAM} view -bS ${OEA}.sam | ${SAM} sort -@ ${NTHREAD} - | ${SAM} view -h -o ${OEA}.sort.sam -
rm ${OEA}.sam
${OEAALG} -s ${SRFILE} -l ${CORR}.fasta -a ${OEA}.sort.sam -t ${NTHREAD} > ${OEA}.fasta
rm ${OEA}.sort.sam