Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate.
The --n_mismatch option will count N's as mismatches in alignments, which may be useful to get sensible alignments for sequences with lots of N's. By default N's are counted as matches. Both the scoring and the counting of matches are affected.
The new --fastq_minqual option for the fastq_filter and fastx_filter commands will discard sequences with any nucleotide with a quality score below the given value. The new --fastq_truncee_rate option for the same commands will truncate sequences at the first position where the number of expected errors per base is below the given value.