Calculate the inner mate-pair distance from two BAM files

With paired-end reads, knowing the inner mate-pair distance is key for some
downstream analyses or mapping. This value can be estimated using wet-lab
techniques, but can also be found empirically. If you map each fragment
separately to a common reference (genome or transcriptome), this command will
calculate the average distance between the fragments.

Reads where one (or both) fragment is unmapped are ignored, as are pairs that
map to different references.

(reference) ===============================================================
                 (frag 1) >>>>>>>>>                      <<<<<<<< (frag 2)
                                   |--------------------|
                                  inner mate-pair distance

This will also work if the reads are aligned in the opposite orientation:

(reference) ===============================================================
                 (frag 2) >>>>>>>>>                      <<<<<<<< (frag 1)
                                   |--------------------|
                                  inner mate-pair distance

or if they overlap:

(reference) ===============================================================
                           (frag 1) >>>>>>>>>
                                         <<<<<<<< (frag 2)
                                        |----|
                                  inner mate-pair distance (negative)


Usage: bamutils innerdist filename1.bam filename2.bam

Options:
  -summary filename       Write all distances out to a file

Note: BAM files must be paired and they must be mapped to the
      same reference and reads must be in the same order.