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# discard STDOUT but capture STDERR in @out
my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1 1>/dev/null`; 
print OUT @out;

# redirect STDOUT to stdout.log and capture STDERR in @out
my @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[
+0] 2>&1 1>stdout.log`;
print OUT @out;
my $stdout = do { local( @ARGV, $/ ) = 'stdout.log'; <> }; # slurp the
+ contents of stdout.log into $stdout
print $stdout;