Determine best default values for jump_score_* parameters

[jdidion]

In #48 we see an example where a single read is aligned to multiple contiguous regions of the same contig (i.e., it is split into primary and supplementary alignments). Modifying the jump penalty (--jump-score-* options) to the following fixes the issue for that specific case. This is a tracking issue to evaluate the parameter settings on multiple examples to see which default values are best (i.e., produce reasonable results for the most cases).

--jump-score-same-contig-and-strand -40 \
--jump-score-same-contig-opposite-strand -80 \
--jump-score-inter-contig -160