Many small updates and bug fixes

* make testcase const and use insert instead of push_backs
* make template parameters all uppercase
* rerun failed tests (underflow) with double precision
* ignore the test_data directory, to modify/add files there you need to use --force. This is to make it difficult for people to add big test files to the repo
* skip all-zero diagonals in cases when read is smaller than the longest read in the testcase
* fixed padding bug where compute_full_prob was using read_length instead of max_original_read_length in testcases where read lengths were variable