push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";
push @args, "-p $options->{ 'cpus' }";
push @args, "-v $options->{ 'mismatches' }"; # DANGER: using seed mismatches as alignment mismatches - may work, may not!
push @args, "-f" if $type eq "FASTA";
push @args, "-p $options->{ 'cpus' }";
-push @args, "--phred64-quals" unless $type eq "FASTA";
+push @args, "--phred33-quals" unless $type eq "FASTA";
if ( defined $options->{ 'max_hits' } ) {
push @args, "-k $options->{ 'max_hits' }";
if ( defined $options->{ 'max_hits' } ) {
push @args, "-k $options->{ 'max_hits' }";