- for( final Sequence seq : seqs ) {
- procSeq( infile.toString(), names, seq );
+ int duplicates = 0;
+ for( final MolecularSequence seq : seqs ) {
+ if ( procSeq( infile.toString(), names, seq ) ) {
+ ++duplicates;
+ }
+ }
+ if ( duplicates > 0 ) {
+ SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 60 );