Refactored code

[yhoogstrate]

The aim of this PR is to refactor the code. Initially the code created sub datasets, because it was expected to export them time-wise and it was very handy for running unit tests. As this is no longer part of the plan, I am refactoring the code to do just the tasks it is supposed to do and which are described in the manuscript: create a large overview of all fusion genes. This refactoring reduces the memory again - this time a really big win for large number of samples.

For now it seems that the output is exactly the same, except for the order of the output.

Todo's:

• [x] Update changelog
• [x] Convert all tests to using (1) the old files [take care of sorting] but use the new function
• [x] Update readme and explain the n-space complexity instead of the number of combinations
• [x] Bump version to 3.*
• [x] Add support for summary output file
• [x] Add more logging to the new objects
• [ ] When all tests are passing, and all points have been addressed, use the following notation in list-output: chr1:10000(-)->chr2:20000(-) to indicate strand and acceptor-donor direction
• No legacy support as the output was in rare cases truncated.

[yhoogstrate]

For subset matching the following happens with the current implementation:

1=F1(A,B)
2=F2(B,C)
3=F3(A,B,C)

3=MF(F1,F3)=>MF(A,B)

then merging F2(B,C) with MF(A,B) results in no match