[BUG] Count duplications in the reference

[Irallia]

So far, we cannot perfectly count duplications in the reference.

The created Example 4 - multiple tandem duplication on read and ref in TEST(junction_detection, analyze_sa_tag) from test/api/detection_test.cpp calculates the wrong number of duplications.
This seems to be a special case, but we may still want to fix it.