use strict;
use warnings;

use POSIX qw{ strftime };

my $organism    = q{WildHaggis};
my $rsite1      = q{ONE};
my $rsite2      = q{TWO};
my $rsite3      = q{THREE};

my $summaryfile = join q{_},
   $organism,
   q{summary_doubleDigest},
   $rsite1,
   $rsite2,
   $rsite3,
   strftime q{%m_%d_%Y.txt}, localtime( time() );

print $summaryfile, qq{\n};

##</code><code>##

WildHaggis_summary_doubleDigest_ONE_TWO_THREE_07_21_2014.txt

##</code><code>##

open my $outFH, q{>}, $radtagfile
   or die qq{open: > $radtagfile: $!\n};

##</code><code>##

for (my $i = 0; $i < scalar @first_fragments; ++$i)

##</code><code>##

foreach my $i ( 0 .. $#first_fragments )