$subject_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
}
$subject_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
}
-$blat_args .= " -tileSize=$options->{ 'tile_size' }";
-$blat_args .= " -oneOff=$options->{ 'one_off' }";
-$blat_args .= " -minIdentity=$options->{ 'min_identity' }";
-$blat_args .= " -minScore=$options->{ 'min_score' }";
-$blat_args .= " -stepSize=$options->{ 'step_size' }";
-$blat_args .= " -maxIntron=$options->{ 'intron_max' }";
-$blat_args .= " -fastMap" if $options->{ 'fast_map' };
-# $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
+if ( $options->{ 'fast_map' } )
+{
+ $blat_args .= " -fastMap";
+}
+else
+{
+ $blat_args .= " -tileSize=$options->{ 'tile_size' }";
+ $blat_args .= " -oneOff=$options->{ 'one_off' }";
+ $blat_args .= " -minIdentity=$options->{ 'min_identity' }";
+ $blat_args .= " -minScore=$options->{ 'min_score' }";
+ $blat_args .= " -stepSize=$options->{ 'step_size' }";
+ $blat_args .= " -maxIntron=$options->{ 'intron_max' }";
+ # $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
+}
$tmp_dir = Maasha::Biopieces::get_tmpdir();
$query_file = "$tmp_dir/blat.seq";
$tmp_dir = Maasha::Biopieces::get_tmpdir();
$query_file = "$tmp_dir/blat.seq";
-$blat_args .= " -t=dnax" if $type eq "protein";
+$blat_args .= " -t=dnax" if $type eq "PROTEIN";
$blat_args .= " -q=$type";
$result_file = "$tmp_dir/blat.psl";
$blat_args .= " -q=$type";
$result_file = "$tmp_dir/blat.psl";