1.map_reads

#!/bin/bash

source globals.sh

if [ ! -e map_reads/final.contigs.fa.bwt ]
then
    cd map_reads
    bwa index final.contigs.fa
    samtools faidx final.contigs.fa
    cd ..
fi

\rm -rf $0.jobs

mkdir -p map_reads
for file in $raw_files
do
	bn=`basename $file`
	base=`echo $bn | sed "s/.fq.gz//g"`
	echo $base
	# run bwa mem, pipe to samtools for SAM to BAM pipe again for only mapped reads and pipe again for sort
	if [ ! -e map_reads/$base.mapped.sorted.bam ]
	then
		echo "bwa mem -t 8 map_reads/final.contigs.fa $file | samtools view -h -b -S /dev/stdin | samtools view -b -F 4 /dev/stdin | samtools sort -m 1000000000 -o map_reads/$base.mapped.sorted.bam /dev/stdin" >> $0.jobs
	fi
done

parallel --jobs 4 --joblog $0.jobs.log < $0.jobs