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use strict;
use warnings;
...
   strftime q{%m_%d_%Y.txt}, localtime( time() );

print $summaryfile, qq{\n};

WildHaggis_summary_doubleDigest_ONE_TWO_THREE_07_21_2014.txt

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

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

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