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[MRG] "Overload" cython consume methods with type introspection #1787

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merged 8 commits into from
Sep 17, 2017
Merged

[MRG] "Overload" cython consume methods with type introspection #1787

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2e32025
"Overload" cython consume methods with type introspection
standage Sep 14, 2017
e2ca266
Cannot figure out ReadParser conditional [skip ci]
standage Sep 14, 2017
921ad7d
Merge branch 'master' into fix/consume-filename-or-parser
standage Sep 14, 2017
5660782
Cython compiles, but now clang chokes
standage Sep 14, 2017
2ced941
Solved compilation issues; now on to the runtime issues
standage Sep 14, 2017
18631bd
Switch consume_seqfile_and_tag_with_labels to overload paradigm
camillescott Sep 14, 2017
ed7556f
Merge branch 'master' into fix/consume-filename-or-parser
standage Sep 15, 2017
f0f61cd
More robust type introspection and error handling
standage Sep 15, 2017
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11 changes: 6 additions & 5 deletions khmer/_oxli/graphs.pxd
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ from libc.stdint cimport uint8_t, uint32_t, uint64_t, uintptr_t

from khmer._oxli.oxli_types cimport *
from khmer._oxli.hashing cimport Kmer, CpKmer, KmerSet, CpKmerFactory, CpKmerIterator
from khmer._oxli.parsing cimport CpReadParser, CpSequence
from khmer._oxli.parsing cimport CpReadParser, CpSequence, FastxParserPtr
from khmer._oxli.legacy_partitioning cimport (CpSubsetPartition, cp_pre_partition_info,
SubsetPartition)
from khmer._oxli.utils cimport oxli_raise_py_error
Expand Down Expand Up @@ -139,15 +139,15 @@ cdef extern from "oxli/hashgraph.hh" namespace "oxli" nogil:

void consume_seqfile_and_tag[SeqIO](const string &,
unsigned int,
unsigned long long)
unsigned long long)

# Ugly workaround. For some reason, Cython doesn't like *just this*
# templated overload -- it chooses whichever was defined last, breaking
# resolution for either strings of FastxParserPtr. So, we rename it on
# the Cython side and give it a real name substitution for code gen.
void consume_seqfile_and_tag_readparser "consume_seqfile_and_tag" [SeqIO](shared_ptr[CpReadParser[SeqIO]],
unsigned int,
unsigned long long)
unsigned long long)

void consume_sequence_and_tag(const string &,
unsigned long long &)
Expand All @@ -160,7 +160,7 @@ cdef extern from "oxli/hashgraph.hh" namespace "oxli" nogil:
unsigned int &,
unsigned long long &) except +oxli_raise_py_error

uintptr_t trim_on_stoptags(string)
uintptr_t trim_on_stoptags(string)

unsigned int traverse_from_kmer(CpKmer,
uint32_t,
Expand All @@ -177,7 +177,7 @@ cdef extern from "oxli/hashgraph.hh" namespace "oxli" nogil:
void load_stop_tags(string, bool) except +oxli_raise_py_error
void extract_unique_paths(string, uint32_t, float, vector[string])
void calc_connected_graph_size(CpKmer, uint64_t&, KmerSet&,
const uint64_t, bool)
const uint64_t, bool)
uint32_t kmer_degree(HashIntoType, HashIntoType)
uint32_t kmer_degree(const char *)
void find_high_degree_nodes(const char *, set[HashIntoType] &) const
Expand Down Expand Up @@ -246,6 +246,7 @@ cdef class Hashtable:
cdef HashIntoType sanitize_hash_kmer(self, object kmer) except -1
cdef bytes _valid_sequence(self, str sequence)
cdef CpKmer _build_kmer(self, object kmer) except *
cdef FastxParserPtr _get_parser(self, object parser_or_filename) except *
cdef list _get_raw_tables(self, uint8_t **, vector[uint64_t])


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