removes reads from a pair of fastq files that are shorter than
    a minimum length. removes both ends of a read if one end falls
    below the threshold while maintaining the order of the reads

def filter_reads_by_length(fq1, fq2, quality_format, min_length=20):
    """
    removes reads from a pair of fastq files that are shorter than
    a minimum length. removes both ends of a read if one end falls
    below the threshold while maintaining the order of the reads

    """

    logger.info("Removing reads in %s and %s that "
                "are less than %d bases." % (fq1, fq2, min_length))
    fq1_out = utils.append_stem(fq1, ".fixed")
    fq2_out = utils.append_stem(fq2, ".fixed")
    fq1_single = utils.append_stem(fq1, ".singles")
    fq2_single = utils.append_stem(fq2, ".singles")
    if all(map(utils.file_exists, [fq1_out, fq2_out, fq2_single, fq2_single])):
        return [fq1_out, fq2_out]

    fq1_in = SeqIO.parse(fq1, quality_format)
    fq2_in = SeqIO.parse(fq2, quality_format)

    out_files = [fq1_out, fq2_out, fq1_single, fq2_single]

    with file_transaction(out_files) as tmp_out_files:
        fq1_out_handle = open(tmp_out_files[0], "w")
        fq2_out_handle = open(tmp_out_files[1], "w")
        fq1_single_handle = open(tmp_out_files[2], "w")
        fq2_single_handle = open(tmp_out_files[3], "w")

        for fq1_record, fq2_record in zip(fq1_in, fq2_in):
            if len(fq1_record.seq) >= min_length and len(fq2_record.seq) >= min_length:
                fq1_out_handle.write(fq1_record.format(quality_format))
                fq2_out_handle.write(fq2_record.format(quality_format))
            else:
                if len(fq1_record.seq) > min_length:
                    fq1_single_handle.write(fq1_record.format(quality_format))
                if len(fq2_record.seq) > min_length:
                    fq2_single_handle.write(fq2_record.format(quality_format))
        fq1_out_handle.close()
        fq2_out_handle.close()
        fq1_single_handle.close()
        fq2_single_handle.close()

    return [fq1_out, fq2_out]