Perl Filehandle problem

test_seek.pl

use IO::File;
use IO::Seekable;
use Data::Dumper;
use strict;
use warnings;

my @files = qw( test_input.txt);

my @fileHndls;
foreach my $file (@files) {
  if ( ! -s $file ) {
           die "File $file does not exist!  Check the command line or the pedigree file for errors!\n";
   }

   my $fh = new IO::File;

   if ( $file =~ /.*\.bz2/ ) {
           if ( $fh->open("bzcat $file |")) {
                   push @fileHndls, $fh;
           } else {
                   die "Could not uncompress file $file on "
                   . "the fly!\n";
           }
   } elsif ( $file =~ /.*\.gz/ ) {
           if ( $fh->open("gunzip -c $file |")) {
                   push @fileHndls, $fh;
           } else {
                   die "Could not uncompress file $file on "
                   . "the fly!\n";
           }
   } else {
           if ( $fh->open("< $file")) {
                   push @fileHndls, $fh;
           } else {
                   die "Could not open file $file!\n";
           }
   }
}

my @chromosomes = qw( chr1 chr2 chr3 chr4 chr5 chr6
                      chr7 chr8 chr9 chr10 chr11 chr12
                      chr13 chr14 chr15 chr16 chr17
                      chr18 chr19 chr20 chr21 chr22
                      chrX chrY chrM );

foreach my $cChrom (@chromosomes) {
  print "processing chrom $cChrom\n";
  my ($cIndex) =  grep { $chromosomes[$_] eq $cChrom } 0..$#chromosomes;
  print "filehandles for $cChrom:\n";
  print Dumper \@fileHndls;
  my $fileHndlsReturn = process($cChrom, $cIndex, \@fileHndls);
  @fileHndls = @$fileHndlsReturn;
}

exit;

sub process {
  my $currChrom = shift;
  my $currIndex = shift;
  my $fileHandlesRef = shift;
  my @fileHandles = @$fileHandlesRef;
  my @newFileHandles;

  for (my $i = 0; $i <= $#fileHandles; $i++) {
   print "  processing file $i\n";
    my $fh = $fileHandles[$i];
    print Dumper $fh;
    while (1) {
      last if ( $fh->eof() );
      $_ = <$fh>;
      next if ($_ =~ /^#|^\s*$|^>locus/ );
      print "$_";
      my @fields = split;
      if ( $fields[3] ne $currChrom ) {
        my ($chrIndex) = grep { $chromosomes[$_] eq $fields[3] } 0..$#chromosomes;
        print "chrIndex $chrIndex currIndex $currIndex\n";
        if ($chrIndex > $currIndex) {
          print "skipping rest of file because greater than current chromosome $currChrom\n";
          $fh->seek(-1,1);
          $newFileHandles[$i] = $fh;
          last;
        } else {
          print "skipping chrom cuz not current.  currChrom $currChrom  line chromosome: $fields[3]\n";
          next;
        }
      }
    } # end while
  } # end foreach fh

  return \@newFileHandles;
}