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hashing.pxd
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hashing.pxd
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from libcpp cimport bool
from libcpp.memory cimport shared_ptr
from libcpp.queue cimport queue
from libcpp.set cimport set
from libcpp.string cimport string
from khmer._oxli.oxli_types cimport *
cdef extern from "oxli/kmer_hash.hh" namespace "oxli":
cdef cppclass CpKmer "oxli::Kmer":
HashIntoType kmer_f
HashIntoType kmer_r
HashIntoType kmer_u
CpKmer(HashIntoType, HashIntoType, HashIntoType)
CpKmer(string, WordLength)
CpKmer(const CpKmer&)
CpKmer()
bool is_forward() const
void set_from_unique_hash(HashIntoType, WordLength)
cdef cppclass CpKmerFactory "oxli::KmerFactory":
KmerFactory(WordLength)
CpKmer build_kmer(HashIntoType) const
CpKmer build_kmer(HashIntoType, HashIntoType) const
CpKmer build_kmer(string &) const
CpKmer build_kmer(const char *) const
cdef cppclass CpKmerIterator "oxli::KmerIterator" (CpKmerFactory):
CpKmerIterator(const char *, unsigned char)
CpKmer first(HashIntoType &, HashIntoType &)
CpKmer next(HashIntoType &, HashIntoType &)
CpKmer first()
CpKmer next()
bool done()
unsigned int get_start_pos() const
unsigned int get_end_pos() const
HashIntoType _hash(const string, const WordLength)
HashIntoType _hash(const string, const WordLength,
HashIntoType &, HashIntoType &)
HashIntoType _hash(const char *, const WordLength)
HashIntoType _hash(const char *, const WordLength,
HashIntoType &, HashIntoType &)
HashIntoType _hash_forward(const char *, WordLength)
string _revhash(HashIntoType, WordLength)
string _revcomp(const string&)
HashIntoType _hash_murmur(const string&, const WordLength)
HashIntoType _hash_murmur(const string&,
HashIntoType&, HashIntoType&)
HashIntoType _hash_murmur_forward(const string&)
cdef extern from "oxli/oxli.hh" namespace "oxli":
ctypedef queue[CpKmer] KmerQueue
ctypedef set[CpKmer] KmerSet
ctypedef bool (*KmerFilter) (CpKmer kmer)
cdef class Kmer:
cdef shared_ptr[CpKmer] _this
cdef readonly str kmer
@staticmethod
cdef Kmer wrap(CpKmer * cpkmer, WordLength K)