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lib/Bio/Kmer.pm  view on Meta::CPAN

our @richseqExt=qw(.gbk .gbf .gb .embl);
our @sffExt=qw(.sff);
our @samExt=qw(.sam .bam);

our $fhStick :shared;      # Helps us open only one file at a time
our $enqueueStick :shared; # Helps control access to the kmer queue


# TODO if 'die' is imported by a script, redefine
# sig die in that script as this function.
local $SIG{'__DIE__'} = sub { my $e = $_[0]; $e =~ s/(at [^\s]+? line \d+\.$)/\nStopped $1/; die("$0: ".(caller(1))[3].": ".$e); };

my $startTime = time();
sub logmsg{
  local $0 = basename $0; 
  my $tid = 0;
  if($iThreads){
    $tid = threads->tid;
  }
  my $elapsedTime = time() - $startTime;
  print STDERR "$0.$tid $elapsedTime @_\n";