====bam文件按照比对到参考基因组正负链拆分====

针对双端reads
  /TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/get_forward_reverse_from_bam_for_paired.sh <in.bam> <prefix>
  
  ####代码
  #!/usr/bin/bash
  
  if [ ! $# -eq 2 ];then
          echo
          echo "Split paired-end reads according to the positive and negative strands based on their alignment to the reference genome"
          echo
          echo "Please note the input format of the file: for example ...."
          echo
          echo "get_forward_reverse_from_bam_for_paired.sh <in.bam> <prefix>"
          echo
          exit 1
  fi
  
  #对双端reads 按正负链拆分
  ###### forward strand
  samtools view -b -f 128 -F 16 $1 > $1.fwd1.bam
  samtools view -b -f 80 $1 > $1.fwd2.bam
  samtools merge -f $2_forward.bam $1.fwd1.bam $1.fwd2.bam
  samtools index $2_forward.bam
  
  ###### reverse strand
  samtools view -b -f 144 $1 > $1.rev1.bam
  samtools view -b -f 64 -F 16 $1 > $1.rev2.bam
  samtools merge -f $2_reverse.bam $1.rev1.bam $1.rev2.bam
  samtools index $2_reverse.bam
  
针对单端数据
  /TJPROJ6/RNA_SH/personal_dir/zhangxin/jiaoben/get_forward_reverse_from_bam_for_single.sh <in.bam> <prefix>
  
  ####代码
  #!/usr/bin/bash
  
  if [ ! $# -eq 2 ];then
          echo
          echo "Split single reads according to the positive and negative strands based on their alignment to the reference genome"
          echo
          echo "Please note the input format of the file: for example ...."
          echo
          echo "get_forward_reverse_from_bam_for_single.sh <in.bam> <prefix>"
          echo
          exit 1
  fi
  ###### forward strand
  samtools view -bF 20 $1 > $2_forward.bam
  samtools index $2_forward.bam
  ###### reverse strand
  samtools view -bf 16 $1 > $2_reverse.bam
  samtools index $2_reverse.bam