boink extensions: or, streaming cDBG stuff

.gitignore

@@ -54,3 +54,4 @@ pep257_report.txt
 .cache/
 khmer/_oxli/*.cpp
 .eggs
+tags

Makefile

@@ -106,11 +106,14 @@ install-dependencies:
 	pip install --requirement doc/requirements.txt
 
 ## sharedobj   : build khmer shared object file
-sharedobj: $(EXTENSION_MODULE)
+sharedobj: $(EXTENSION_MODULE) $(CYTHON_MODULE)
 
 $(EXTENSION_MODULE): $(CPPSOURCES) $(CYSOURCES)
 	./setup.py build_ext --inplace
 
+$(CYTHON_MODULE): $(CPPSOURCES) $(CYSOURCES)
+	./setup.py build_ext --inplace
+
 coverage-debug: $(CPPSOURCES)
 	export CFLAGS="-pg -fprofile-arcs -ftest-coverage -O0"; ./setup.py \
 		build_ext --debug --inplace --libraries gcov
@@ -144,6 +147,7 @@ clean: FORCE
 	rm -rf __pycache__/ khmer.egg-info/
 	@find ./ -type d -name __pycache__ -exec rm -rf {} +
 	@find ./khmer/ -type f -name *$(MODEXT) -exec rm -f {} +
+	@find ./khmer/_oxli/ -type f -name *.so -exec rm -f {} +
 	-rm -f *.gcov
 
 debug: FORCE
@@ -285,6 +289,8 @@ install-liboxli: liboxli
 	cd src/oxli && $(MAKE) install PREFIX=$(PREFIX)
 	mkdir -p $(PREFIX)/include/khmer
 	cp -r include/khmer/_cpy_*.hh $(PREFIX)/include/khmer/
+	cp include/oxli/oxli_exception_convert.hh $(PREFIX)/include/oxli/
+	cp third-party/rollinghash/*.h $(PREFIX)/include/oxli/
 
 # Runs a test of liboxli
 libtest: FORCE

include/khmer/_cpy_khmer.hh

@@ -44,7 +44,6 @@ Contact: [email protected]
 
 #include <Python.h>
 
-#include <iostream>
 
 #include "_cpy_utils.hh"
 
@@ -77,20 +76,6 @@ Contact: [email protected]
 
 namespace khmer {
 
-PyObject * forward_hash(PyObject * self, PyObject * args);
-
-PyObject * forward_hash_no_rc(PyObject * self, PyObject * args);
-
-PyObject * reverse_hash(PyObject * self, PyObject * args);
-
-PyObject * murmur3_forward_hash(PyObject * self, PyObject * args);
-
-PyObject * murmur3_forward_hash_no_rc(PyObject * self, PyObject * args);
-
-PyObject * reverse_complement(PyObject * self, PyObject * args);
-
-PyObject * get_version_cpp( PyObject * self, PyObject * args );
-
 extern PyMethodDef KhmerMethods[];
 
 }

include/oxli/assembler.hh

@@ -53,6 +53,7 @@ namespace oxli
 class Hashgraph;
 class LabelHash;
 
+
 /**
  * \class LinearAssembler
  *
@@ -78,8 +79,10 @@ public:
 
     WordLength _ksize;
     const Hashgraph * graph;
+    std::shared_ptr<SeenSet> global_visited;
 
-    explicit LinearAssembler(const Hashgraph * ht);
+    explicit LinearAssembler(const Hashgraph * ht,
+                             std::shared_ptr<SeenSet> global_visited = nullptr);
 
     virtual std::string assemble(const Kmer seed_kmer,
                                  const Hashgraph * stop_bf = 0) const;
@@ -97,12 +100,36 @@ public:
 // The explicit specializations need to be declared in the same translation unit
 // as their unspecialized declaration.
 template<>
-std::string LinearAssembler::_assemble_directed<TRAVERSAL_LEFT>(AssemblerTraverser<TRAVERSAL_LEFT>
-        &cursor) const;
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_LEFT>(AssemblerTraverser<TRAVERSAL_LEFT> &cursor) const;
 
 template<>
-std::string LinearAssembler::_assemble_directed<TRAVERSAL_RIGHT>(AssemblerTraverser<TRAVERSAL_RIGHT>
-        &cursor) const;
+std::string LinearAssembler::_assemble_directed<TRAVERSAL_RIGHT>(AssemblerTraverser<TRAVERSAL_RIGHT> &cursor) const;
+
+
+class CompactingAssembler: public LinearAssembler
+{
+public:
+
+    explicit CompactingAssembler(const Hashgraph* ht,
+                                 std::shared_ptr<SeenSet> global_visited=nullptr) 
+        : LinearAssembler(ht, global_visited) {}
+
+    virtual std::string assemble(const Kmer seed_kmer,
+                                          const Hashgraph * stop_bf) const;
+
+    virtual std::string assemble_right(const Kmer seed_kmer,
+                               const Hashgraph * stop_bf = 0) const;
+
+    virtual std::string assemble_left(const Kmer seed_kmer,
+                              const Hashgraph * stop_bf = 0) const;
+
+    template<bool direction>
+    std::string _assemble_directed(CompactingAT<direction>& cursor) const 
+    {
+        return LinearAssembler::_assemble_directed<direction>(cursor);
+    }
+};
+typedef CompactingAssembler CpCompactingAssembler;
 
 
 /**
@@ -160,7 +187,6 @@ public:
     explicit JunctionCountAssembler(Hashgraph * ht);
     ~JunctionCountAssembler();
 
-
     StringVector assemble(const Kmer seed_kmer,
                           const Hashtable * stop_bf=0) const;