Stable release

This released the final stable version used by the Sierra project. Several changes was made in this version to increase the performance and fine-tune the alignment results.

1. Identify simple alignment during the boundary detecting process. An alignment was called "simple" if there was not a single indel or frameshift. A simple alignment reduced the space complexity from O(mn) to O(n) by tracing back the alignment path arithmetically without using any matrix.
2. Reduce matrix space usage by half by removing the not used scores.
3. Semiglobal alignment was introduced to the core algorithm by not penalizing gaps at the beginning and the end of the alignment.
4. Implement continuous integration with TravisCI and CodeCov.
5. Fine-truning of the RT69 indel scores for HIV-1 pol sequences.