Todos

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• [ ] remove filenames from HIBF, after testing with raptor
  • [x] Add #ifdef RAPTOR_OLD_HIBF for serialization and remove filenames from lib (#82)
  • [ ] Finally remove #ifdef RAPTOR_OLD_HIBF afterwards
• [ ] documentation
• [ ] decide what is public and accessible
• [ ] read_from/write_to should have error handling. Should it always consume until the appropriate prefix appears?

Done:

• [x] count interface for hibf (#119)
• [x] IBF construction should get a similar ctor as the HIBF (#80)
• [x] HIBF sets defaults and correct tmax (config.t_max = 0 -> warning? set default like chopper?) (#66)
• [x] config always const & (#66)
• [x] error if number_of_bins == 0 in config (#66)
• [x] remove warning for tmax (#66) (should we?)
• [x] HIBF should be constructable from a layout file (#50)
  • Therefore HIBF lib needs to be able to read and write a layout (from chopper)
• [x] Rename hibf.bulk_containes to hibf.membership_for (#55)
• [x] directory structure (#54)
• [x] namespaces
  • [x] Renamed to hibf -> seqan::hibf (#51)
  • [x] check that subnamespaces are consistent (#58)
• [x] store timer in config (#61)
• [x] remove lemon dependency (#56)
• [x] import chopper tests

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• [x] Check if ctors should be again removed (Added in #41) (#67)
• [x] review config
  • [x] Check if members can be removed
  • [x] Add config validation (#78)
  • We have also discussed the following: Should the IBF get its own class? Probably yes but well wait for the dynamic_hibf or the paritioned_hibf to have more use cases and think more about the config design Should the general/filter config be separated from the layout config? No, because they share e.g. input_fn and number_of_user_bins and it would not be possible to check if input_fn is exactly the same. Or if ONLY in filter config, then it is misleading because the layout needs the input.

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Config

double max_rearrangement_ratio{0.5};
bool disable_estimate_union{false};
bool disable_rearrangement{false};

max_rearrangement_ratio == 0.0 means disable_rearrangement == true.

Estimate union should improve layout.

How much runtime does union estimate and rearrangement add?

Maybe always do union estimate. max_rearrangement_ratio controls rearrangement.

double max_rearrangement_ratio{0.5};
// bool disable_estimate_union{false}; REMOVED
// bool disable_rearrangement{false}; REMOVED