app guide

Application Level API

The BLISS library contains high level api for integration into exisiting or new applications.

The design goals of these APIs are

1. semantically clear
2. simple to use
3. hides (most of) complexity of parallel backend
4. easy to extend

Kmer Index

API

Three Kmer Indexes classes are currently provided. All use MPI and OpenMP as their parallel backend.

• KmerCountIndex
• KmerPositionIndex
• KmerPositionAndQualityIndex

Each of these classes provide the following functions:

void build(const std::string &filename, const int &nthreads)
void sendQuery(const KmerType & kmer)
void flushQuery()
void query(const std::vector<KmerType>& kmers)
MapType& getLocalIndex()
void finalize()