For #244, Fragments were incorrect order and incomplete

[arahuja]

There were two issues here:

1. the fragments were indexed in the wrong order (the list by generated by placing the NEXT fragment at the front of the list and giving that index 0.
2. Only the first fragment was taken off on each addition (assuming that the sequence string was not more than 2x fragment length) If it was the rest of the sequence would not taken off until the next sequence was adding making the last sequence very long and >> maxFragmentLength possibly.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/326/

[massie]

Thanks, Arun!