This thread is for still unanswered questions about program implementation.
1. Names of sequences in input files:
Will all of them start with: >test_sequence_?
What is the biggest number in the name of the test sequence?
What is the largest and the smallest minMatchLength, that will be tested?
3. Characters in files:
Do we have to check them or all of them will be valid?
If I have missed something, feel free to add...