# Initialization
# Read input file, calls to system('bowtie2', ...) and system('samtools', ...)
use strict;
use warnings;
use Carp qw(confess);
use Sys::Info::Device::CPU; 


use Sys::Info::Constants qw( :device_cpu );
my $info = Sys::Info->new;
my $cpu  = $info->device( CPU => {} );
my $nthreads = $cpu->count;
print "$nthreads threads\n";

while ($nthreads--) {
    my $pid = fork;
    confess ("Can't fork: $!") unless defined $pid;
    if (! $pid) {
	print "child process: $$\n";      # this line never gets executed by some of the children
	# Do a bunch of processing using intermediate files as input, using Bio::DB::Sam->get_features_by_location() to access intermediate files
	exit 0;
    }
}

# parent continues here:
my $pid = 0;
my $ok = 1;
while ($pid != -1) {
  $pid = wait;
  last if $pid == -1;

  my $err=$?;
  if ($err) {
    print("one of the children died: pid=$pid, err=$err\n");
    $ok = 0;
  }
}
if (! $ok) {
  confess "some child processes died.";
}
print "all done, yay\n";