Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}
+close $fh_out if $fh_out;
+
foreach $format ( @{ $options->{ 'formats' } } )
{
print STDERR qq(Creating format: $format for $genome ... ) if $options->{ 'verbose' };
- if ( $format =~ /^fasta$/i ) { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/fasta/$genome.index" ) }
+ if ( $format =~ /^fasta$/i ) { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", $fasta_dir, "$genome.index" ) }
elsif ( $format =~ /^blast$/i ) { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) }
elsif ( $format =~ /^blat$/i ) { warn "BLAT FORMAT NOT IMPLEMENTED" }
elsif ( $format =~ /^vmatch$/i ) { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) }
print STDERR qq(done.\n) if $options->{ 'verbose' };
}
-close $fh_out if $fh_out;
-
Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );