#!/usr/bin/perl -w
use warnings;
use strict;
use Data::Dumper;




# BWA alignment output (.sam)

my %bwa = ();
my $file1 = shift;
open (FILE1, "$file1") || die "Failed to open $file1 for reading : $!"; # Open second file

while (<FILE1>) { # Reading second hash
    if ($_ =~ /^[^@]/s) {
    chomp;
    my @line = split /\s+/, $_;
    my $ID;
    if ($line[2] =~ /[^*]/) {
    $ID = $line[0];
	push @{$bwa{$ID}}, @line[2,5,12,15,16,17,18];
    }
  }
}
close FILE1 || die "Failed to close $file1 : $!";




# ORIGINAL Reference Amplicon File (.fa)

my %Amp = ();
my $file2 = shift;
open (FILE2, "$file2")|| die "Failed to open $file2 for reading : $!"; # Open first file
local $/= ">";
my $first=<FILE2>;
while (<FILE2>) { # Reading first hash
	chomp;
	my ($ID, $Seq) = split("\n");
	$Amp{$ID} = $Seq
}
close FILE2 || die "Failed to close $file2 : $!";


# ORIGINAL Input FASTQ Sequencing File (.fq)

my %Input = ();
my $file3 = shift;
open (FILE3, "$file3")|| die "Failed to open $file3 for reading : $!"; # Open first file
local $/= "@";
$first=<FILE3>;
while (<FILE3>) { # Reading first hash
	chomp;
	my ($ID, $Seq,undef,undef) = split("\n");
	$Input{$ID} = $Seq;
}
close FILE3 || die "Failed to close $file3 : $!";


foreach my $ID (keys %bwa)
{
	if (exists $Input{$ID}){
			print "Key : $ID\t AMP:\t$Amp{$bwa{$ID}[0]}\nInput\t$Input{$ID}" if (exists $Amp{$bwa{$ID}[0]});
	}
}