folder=$1
handel=`echo $folder | sed 's/\.out//g'`

for i in $folder/*/alignments.sam
do
j=`echo $i | sed 's/\.sam/\.bam/g'`
echo -e "$j"
samtools view -Sb $i > $j
done


samtools merge $handel.bam $folder/*/alignments.bam


samtools sort $handel.bam  $handel.sort

rm -r $folder
rm -r $handel.log
rm -r $handel.sh