$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+`cd "$ENV{ BP_C }/Maasha/src" && make`; # FIXME OMG this is crufty!
+
$tmp_dir = Maasha::Biopieces::get_tmpdir();
$bed_file = "$tmp_dir/assemble_tag_contigs.bed";
$tmp_dir = Maasha::Biopieces::get_tmpdir();
$bed_file = "$tmp_dir/assemble_tag_contigs.bed";