handle many SAM files (批量处理SAM文件)

#sam2bam,bam2sort,bam2index
screen -S yourname
for i in `ls *.sam`;
do
j=${i/\.sam/};
echo "samtools view -b -S $j.sam > $j.bam
samtools sort $j.bam sorted_$j
samtools index sorted_$j.bam" >> $j.sh
done

for i in `ls *.sh`;do echo "bash $i" >> total.sh;done

ParaFly -c total.sh -CPU 9
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