Version 0.5.1 bugfixes: - paired_end_read_merger don't crash on nested reads due to quality issue (heavy quality-timming or aligner soft-clipping) one read can be entirely fit within it's paired mate - aln2basecnt don't crash on CDC IRMA's bam with N cigar operators SAMv1: For mRNA-to-genome alignment, an N operation represents an intron. For other types of alignments, the interpretation of N is not defined.