6.map_reads_to_bins

#!/bin/bash

bin_directory=metabat

source globals.sh

DIR=map_reads_to_bins

mkdir -p $DIR

bins=`ls metabat/bin.*.fa`

\rm -rf $0.jobs
cd $DIR

for file in $bins
do
	bin=`basename $file`
	echo $bin
	mkdir -p $bin.dir
	cp ../$file $bin.dir
	cd $bin.dir
	if [ ! -e $bin.bwt ]
	then
    		bwa index $bin
		samtools faidx $bin
	fi
	# run bwa mem, pipe to samtools for SAM to BAM pipe and  pipe again for sor
	echo "(zcat $pe_files | bwa mem -t 8 $DIR/$bin.dir/$bin /dev/stdin | samtools view -h -b -S /dev/stdin | samtools sort -n -m 1000000000 -o $DIR/$bin.dir/$bin.namesorted.bam /dev/stdin)" >> ../../$0.jobs
	cd ..
done

cd ..

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