1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
|
#include <pybind11/pybind11.h>
#include <pybind11/operators.h>
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <kmc_file.h>
namespace py = pybind11;
struct Count
{
uint64 value;
};
struct CountVec
{
std::vector<uint32> value;
};
struct LongKmerRepresentation
{
std::vector<uint64> value;
};
PYBIND11_MODULE(py_kmc_api, m) {
m.doc() = "Python wrapper for KMC_API."; // optional module docstring
py::class_<LongKmerRepresentation>(m, "LongKmerRepresentation")
.def(py::init<>())
.def_readwrite("value", &LongKmerRepresentation::value);
py::class_<CountVec>(m, "CountVec")
.def(py::init<>())
.def_readwrite("value", &CountVec::value);
py::class_<Count>(m, "Count")
.def(py::init<>())
.def_readwrite("value", &Count::value);
py::class_<CKMCFileInfo>(m, "KMCFileInfo")
.def(py::init<>())
.def_readwrite("kmer_length", &CKMCFileInfo::kmer_length)
.def_readwrite("mode", &CKMCFileInfo::mode)
.def_readwrite("counter_size", &CKMCFileInfo::counter_size)
.def_readwrite("counter_size", &CKMCFileInfo::counter_size)
.def_readwrite("lut_prefix_length", &CKMCFileInfo::lut_prefix_length)
.def_readwrite("signature_len", &CKMCFileInfo::signature_len)
.def_readwrite("min_count", &CKMCFileInfo::min_count)
.def_readwrite("max_count", &CKMCFileInfo::max_count)
.def_readwrite("both_strands", &CKMCFileInfo::both_strands)
.def_readwrite("total_kmers", &CKMCFileInfo::total_kmers);
py::class_<CKmerAPI>(m, "KmerAPI")
.def(py::init<uint32>(), py::arg("length") = 1)
.def(py::init<const CKmerAPI&>())
.def("assign", &CKmerAPI::operator=)
.def(py::self == py::self)
.def(py::self < py::self)
.def("get_asci_symbol", &CKmerAPI::get_asci_symbol)
.def("get_num_symbol", &CKmerAPI::get_num_symbol)
.def("to_string", [](CKmerAPI& ptr) {return ptr.to_string(); })
.def("to_string", [](CKmerAPI& ptr, char* str) { ptr.to_string(str); })
.def("__str__", [](CKmerAPI& ptr) {return ptr.to_string(); })
.def("to_string", [](CKmerAPI& ptr, std::string& str) { ptr.to_string(str); })
.def("to_long", [](CKmerAPI& ptr, LongKmerRepresentation& res) {ptr.to_long(res.value); })
.def("reverse", &CKmerAPI::reverse)
.def("get_signature", &CKmerAPI::get_signature)
.def("from_string", [](CKmerAPI& ptr, const char* str) { return ptr.from_string(str); })
.def("from_string", [](CKmerAPI& ptr, const std::string& str) { return ptr.from_string(str); });
py::class_<CKMCFile>(m, "KMCFile")
.def(py::init<>())
.def("OpenForRA", &CKMCFile::OpenForRA)
.def("OpenForListing", &CKMCFile::OpenForListing)
.def("ReadNextKmer", [](CKMCFile& ptr, CKmerAPI& kmer, Count& count) {return ptr.ReadNextKmer(kmer, count.value); })
.def("Close", &CKMCFile::Close)
.def("SetMinCount", &CKMCFile::SetMinCount)
.def("GetMinCount", &CKMCFile::GetMinCount)
.def("SetMaxCount", &CKMCFile::SetMaxCount)
.def("GetMaxCount", &CKMCFile::GetMaxCount)
.def("GetBothStrands", &CKMCFile::GetBothStrands)
.def("KmerCount", &CKMCFile::KmerCount)
.def("KmerLength", &CKMCFile::KmerLength)
.def("RestartListing", &CKMCFile::RestartListing)
.def("Eof", &CKMCFile::Eof)
.def("CheckKmer", [](CKMCFile& ptr, CKmerAPI& kmer, Count& count) { return ptr.CheckKmer(kmer, count.value); })
.def("IsKmer", &CKMCFile::IsKmer)
.def("ResetMinMaxCounts", &CKMCFile::ResetMinMaxCounts)
.def("Info", [](CKMCFile& ptr, CKMCFileInfo& info) {return ptr.Info(info); })
.def("Info", [](CKMCFile& ptr) { CKMCFileInfo info; ptr.Info(info); return info; })
.def("GetCountersForRead", [](CKMCFile& ptr, const std::string& read, CountVec& counters) {
return ptr.GetCountersForRead(read, counters.value);
})
;
}
|
