$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
if ( defined $options->{ 'genome' } ) {
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
if ( defined $options->{ 'genome' } ) {
- $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+ $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bwa/$options->{ 'genome' }";
} elsif (defined $options->{ 'index_name' } ) {
$index = $options->{ 'index_name' };
}
} elsif (defined $options->{ 'index_name' } ) {
$index = $options->{ 'index_name' };
}