trim_reads_move_BC

#!/usr/bin/env perl
use String::Approx qw(amatch);
use String::Approx 'aindex';
use String::Approx 'adist';
$num_args = $#ARGV + 1;
if ($num_args != 1) {
	$BARCODE_LENGTH = 6;
} else {
	$BARCODE_LENGTH = $ARGV[0];
}
my $line_index = -1;
my @array;
while(my $line = <STDIN>) {
	chomp($line);
	$line_index = $line_index + 1;
	if ($line_index == 4) {
		foreach(@array) {
			print $_ . "\n";
		}
		$line_index = 0;
	}
	@array[$line_index] = $line;
	if ($line_index == 3) {
		@array[0] = @array[0] . " BQ:Z:" . substr $line, 0, $BARCODE_LENGTH;
		@array[$line_index] = substr $line, $BARCODE_LENGTH;
	} elsif ($line_index == 0) {
		 @array[$line_index] = (split(/\s+/,$line))[0];
	} elsif ($line_index == 1) {
		@array[0] = @array[0] . " BC:Z:" . substr $line, 0, $BARCODE_LENGTH;
		$line = substr $line, $BARCODE_LENGTH;
		my $length = length($line);
		$line = uc $line;
		$index = aindex("AGATCGGAAGAGCACAC", ["3"], $line) ;
		$dist = adist("AGATCGGAAGAGCACAC", $line) ;
		$index2 = aindex("AGATCGGAAGAGCGTCG", ["3"], $line) ;
		$dist2 = adist("AGATCGGAAGAGCGTCG", ["3"], $line) ;
		if ($dist2 < $dist) {
			$index = $index2;
			$dist = $dist2;
		}
		if ($index > -1 && $index < $BARCODE_LENGTH + 2) {
			@array[1] = (("N" x $length));
		} elsif ($index == -1) {
			@array[1] = "$line";
		} else {
			my $putative_AGA = substr $line, $index - $BARCODE_LENGTH, 3;
			$extra_dist = adist("AGA", $putative_AGA);
			#print "extra dist : $extra_dist\n";
			$dist = $dist + $extra_dist;
			#print "dist : $dist\n";
			if ($dist <= 3) {
#remove 6 bases that correspond to variable + constant barcode + an extra 4 bases
				my $sub = substr $line, 0, $index - $BARCODE_LENGTH > 0 ? $index - $BARCODE_LENGTH : 0;
				$sub = $sub . ("N" x ($length - length($sub)));
				@array[1] = "$sub";
			} else {
				@array[1] = "$line";
			}
		}
	} else {
		@array[$line_index] = $line;
	}
}
foreach(@array) {
	print $_ . "\n";
}