- mc = MsaCompactor.reduceLength( msa, length, step, realign, path_to_mafft, out );
+ if ( length >= msa.getLength() ) {
+ ForesterUtil.fatalError( PRG_NAME, "target MSA length (" + length
+ + ") is greater than or equal to MSA original length (" + msa.getLength() + ")" );
+ }
+ // TODO if < shortest seq -> error
+ mc = MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );