Option to treat each read as its own fragment

[snystrom]

Some assays or sequencing methodologies (long read technology like PBio or ONT) may be more appropriate to consider each read as a fragment. Add a flag -l that enables this behavior.

This may require some additional reworking of some VMatrix internals to correctly grab the insert_size. Need to do some tests to make sure these behave as expected.

If implemented correctly, the -f options should work seamlessly.