#!/usr/bin/perl
use POSIX; 
use IO::File;

my %counts = {};

my $bGood   = 0;

my %keys = {};

my $count = 0;
my $fileName = 0;

my $primer  = &translateIUPAC($ARGV[0]);
my $keyFile = $ARGV[1];

open(FILE, "$keyFile") or die;

while($line = <FILE>){
    chomp($line);

    @tokens = split(/,/,$line);

    my $tag = $tokens[1];

    $fileName = $tokens[0].".raw";
    #my $fileName = "Seq${count}.fa";

    my $fh = IO::File->new();

    open($fh, ">$fileName") or die "Can't open $fileName\n";

    print $fh "$count $tag $fileName\n";

    $keys{$tag} = $fh;

    #close($fh);

    $count++;
}
close(FILE);

my $flowSeq = "TACG";


while(my $line = <STDIN>){
    chomp($line);
 
    if($line =~ />(.*)/){
	my $id = $1;
	my $clipleft  = -1;
	my $clipright = -1;
	my $flowRef  = -1;
	my $length   = -1;
	my $sequence = -1;
	
	$line = <STDIN>; $line = <STDIN>;
	chomp($line);

	if($line =~ /\s+Clip:\s+(\d+)\s+(\d+)/){
	  $bGood = 1;
	  $clipleft = $1; $clipright = $2;
	  $line = <STDIN>; chomp($line);
	  if($line =~ /Flows:\s+(.*)/){
	
	    my @tokens = split(/\s+/,$1);
	    
	    $flowRef = \@tokens;
	  }
	  else{
	    $bGood = 0;
	  }
	}
	else{
	  $bGood = 0;
	  #printf "Format error $line\n";
	}


	$line = <STDIN>; chomp($line);
	if($line =~ /Index:\s+(.*)/){
	  my @tokens = split(/\s+/,$1);
		
#	  print "@tokens\n";	
#	  shift(@tokens);
	    
#	  print "$clipright @tokens\n";
	  $length = $tokens[$clipright - 1];
#	  print "$clipright $length\n";
	  
	}
	else{
	  $bGood = 0;
	  #printf "Format error $line\n";
	}
	$line = <STDIN>; chomp($line);
	if($line =~ /Bases:\s+(\w+)$/){
#	  print "$1\n";
	  $sequence = $1;
	  #
	}
	else{
	  $bGood = 0;
	  #printf "Format error $line\n";
	}

	my $read = flowToSeq($length,@{$flowRef});
#	print "$bGood $length $read @{$flowRef}\n";
	if($bGood == 1 && $read =~ /^TCAG(\w*)$primer.*$/){
	  my $tag = $1;
	  if($keys{$tag} ne undef){
	    my $fh = $keys{$tag};
	    
	    print $fh ">$id\n$length @{$flowRef}\n";

	    $counts{$tag}++;
	  }
	  else{
	    print STDERR ">$id\n$sequence\n";
	  }
	}
      }
  }

my $total = 0;
foreach $key (keys %counts){
    my $count = $counts{$key};
    if($count > 0){
	print "$key $count\n";
	$total += $count;
    }
}
print "$nReads $total\n";

sub flowToSeq()
{
    my ($length, @flowgram) = @_;
    my $retSeq = "";

    for(my $i = 0; $i < $length; $i++){
	my $signal = floor($flowgram[$i] + 0.5);
	my $base   = substr($flowSeq, $i % 4, 1);

	for(my $j = 0; $j < $signal; $j++){
	    $retSeq .= $base;
	}
    }

    return $retSeq;
}

sub translateIUPAC()
{
  my ($seq) = @_;

  $seq=~s/W/\[AT\]/g;
  $seq=~s/B/\[CGT\]/g;
  $seq=~s/S/\[GC\]/g;  
  $seq=~s/N/\[ACTG\]/g;
  $seq=~s/Y/\[CT\]/g;
  $seq=~s/R/\[AG\]/g;
  $seq=~s/D/\[AGT\]/g;
  $seq=~s/H/\[ACT\]/g;
  $seq=~s/M/\[AC\]/g;
  $seq=~s/K/\[GT\]/g;
  $seq=~s/V/\[ACG\]/g;
  return $seq;
}