my $input = 'fragments.txt';
my %split;

open(my $infile, '<', $input)
    or die "Cannot open file '$input' for reading: $!";

build_hash($_) while <$infile>;

close $infile
    or die "Cannot close file '$input': $!";

build_hash(length($sequence) + 1);

sub build_hash
{
    use feature 'state';

    state $old     =  0;
    state $cnt     =  1;
    my   ($line)   =  @_;
    my    $gap     =  $line - $old;
    my    $start   =  $old  + 1;
    my    $end     = ($gap  > 2) ? $line - 1 : $start;
    $split{$cnt++} = [$start .. $end] if $gap >= 2;
          $old     =  $line;
}