#!/opt/local/bin/perl

use Bio::Seq;
use Bio::DB::Sam;
use PDL;
use PDL::Char;
$PDL::SHARE = $PDL::SHARE;

# Load bam file
my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );

for my $read (@allReads) {
	# Get read and target sequences
	( $ref, $matches, $query ) = $read->padded_alignment;
	my $target = PDL::Char->new("$ref");
	for my $str ("$query") {
		my $match = PDL::Char->new($str);
		my @diff  = which( $match != $target )->list;
		# Print read name and mismatching positions
		print $read->qname,': ', "@diff\n";
	}
}