TODO

ToDo
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- [X] Filtering
- [X] Filtering tests
- [ ] Proper docs (API etc.)
- [X] README (compiling, clang format, run tests)
- [X] Alphabet tests
- [ ] Allow WorkerQueue Enqueue with rvalues
- [X] Global Search Tests
- [X] Alnout Tests
- [ ] Masking of low-quality sequence regions (e.g. ATATATATATA)
- [ ] Try out vector instead of deque
- [ ] Find final name
- [ ] Namespacing (after final name was determined)
- [ ] Pick OS license
- [X] GZIP input support
- [ ] GZIP output support
- [ ] SAM Output
- [ ] Alnout: Sort by id% for multiple hits!
- [ ] Performance: Reject candidate immediately if all HSP similarities lower than requested similarity
- [ ] Allow overwriting of word size on cmd line!
- [ ] Drop CPP so we can only use headers

Wishlist
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- [ ] Camila's idea: Add special coding gap model: Penalize gaps which shift the reading frame heavily, but penalize gaps with 3nt, 6nt etc. which delete AAs less