FM-Index

We have to main indices. The FMindex and the BiFMIndex.

As a first parameter, they take a string implementation with an alphabet size.

Example

Creates a BiFMIndex that covers the 4 base nucleotide A, C, G, T represented as 1, 2, 3, 4. The BiFMIndex and the FMIndex require the 0 for special internal purposes. It is possible to use it in a reference text, but it will not be considered during a search.

int main() {
    auto ref = std::vector<std::vector<uint8_t>>{
        {1, 1, 1, 2, 2, 2, 3, 2, 4, 1, 1, 1}, // seqId 0
        {1, 2, 1, 2, 3, 4, 3},                // seqId 1
    };

    // Pick String with Ranksupport implementation
    using String = fmc::string::FlattenedBitvectors_512_64k<5>; // 5 number of different characters

    // Creating an bidirectional FM-Inddex
    auto index = fmc::BiFMIndex<String>{reference, /*.samplingRate=*/16, /*.threadNbr=*/1};
}

Advanced

Different FM-Indices classes exist:

• fmindex_collection::FMIndex<OccTable Table, typename TCSA>
• fmindex_collection::BiFMIndex<OccTable Table, typename TCSA>
• fmindex_collection::ReverseFMIndex<OccTable Table, typename TCSA>
• fmindex_collection::RBiFMIndex<OccTable Table, typename TCSA> (what does this one do?)