view rapsodyn/PileupVariant.pl @ 28:fefe6d89dbf1 draft

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#!/usr/bin/perl
use strict;

my $inputfile = $ARGV[0];
open(IF, $inputfile)  or die("Can't open $inputfile\n");

#Extraction des variants
my $nb_line=0;
while (my $line=<IF>){
	my $test = $line;
	$test =~ s/\$//g; #the read start at this position
	$test =~ s/\^.//g; #the read end at this position followed by quality char
	my @field = split(/\s+/,$test);
	
	if ($field[4]=~/[ATGCN]/i){
		print $line;
	}
}
close(IF);