# V5: Inline::C
#!/opt/local/bin/perl
use strict;
use Inline C => Config => BUILD_NOISY => 1;
use Inline C => <<'END_C', NAME => 'dnacmp', CLEAN_AFTER_BUILD => 0;

void dnacmp( char *a, char *b ) {
    int n = 0;
    Inline_Stack_Vars;

    Inline_Stack_Reset;
    while( *a && *b ) {
        if( *a != *b ) {
            Inline_Stack_Push( sv_2mortal( newSVpvf( "%d:%c:%c", n, *a, *b ) ) );
        }
        a++; b++; n++;
    }
    Inline_Stack_Done;
    return;
}

SV *dnacmp2( char *a, char *b ) {
    SV *res = newSVpv( "", 0 );
    int n = 0;

    while( *a && *b ) {
        if( *a != *b )
            sv_catpvf( res, "%d:%c:%c ", n, *a, *b );
        ++a, ++b, ++n;
    }
    return res;
}
END_C

use Bio::Seq;
use Bio::DB::Sam;

my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );
for my $read (@allReads) {
	( $ref, $matches, $query ) = $read->padded_alignment;
	print $read->qname, "\n", dnacmp2('$ref', '$query');
}

##</code><code>##


Global symbol "$query" requires explicit package name at mutations.pl line 133.
Execution of mutations.pl aborted due to compilation errors.
Pradeep-Bandarus-MacBook-Pro:test pradeepbandaru$ perl mutations.pl
Global symbol "$ref" requires explicit package name at mutations.pl line 133.
Global symbol "$matches" requires explicit package name at mutations.pl line 133.
Global symbol "$query" requires explicit package name at mutations.pl line 133.
Execution of mutations.pl aborted due to compilation errors.