samtools mpileup原始结果文件处理，非bcf/vcf格式

samtools mpileup处理的原始结果向来比较麻烦，写了一个小程序只生成碱基reads，但不进行任何过滤：

#!/usr/bin/env perl 
use strict;
use warnings;
use Getopt::Long;

my %opt;
GetOptions(\%opt, "i=s", "o=s", "sd=s", "ad=s", "aq=s");

my $usage = <<"USAGE";

	Usage: perl $0 -i <pileup>  [options]
	CreationTime: 
	ModifyTime: 
	Note: 

	Options:
	-i			input file

	eg: perl $0 -i file.pileup > result

USAGE

die $usage if(!$opt{i});

open IN, ($opt{i} =~ /\.gz$/) ? "gzip -dc $opt{i} |" : $opt{i} or die $!;
my (@tmp, @qual, @base, %index);
while(<IN>)
{
	chomp;
	@tmp = split /\t/;
	next if($tmp[2] eq "N");

	while($tmp[4] =~ /[\+-](\d+)[ATCGNatcgn]+/)
	{
		$tmp[4] =~ s/[\+-]\d+[ATCGNatcgn]{$1}//;
	}
	$tmp[4] =~ s/\^\S//g; #\<\=\>\-\!\?\/\'\"\)\(\]\[\*\\\.\+,;:@&#%0-9A-Z