S4 (#3)

* Update spoa to 4.0.0 and build for portability
nanoporetech · Oct 2, 2020 · 5439edc · 5439edc
1 parent 5c5f4bb
commit 5439edc
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Showing 4 changed files with 17 additions and 18 deletions.
diff --git a/Makefile b/Makefile
@@ -1,6 +1,8 @@
+
 build:
+	cmake --version
 	mkdir -p src/build
-	cd src/build && cmake -DCMAKE_BUILD_TYPE=Release -D CMAKE_CXX_FLAGS="-fPIC" .. && make
+	cd src/build && cmake -D optimize_for_portability=ON -DCMAKE_BUILD_TYPE=Release -D CMAKE_CXX_FLAGS="-I ../vendor/cereal/include/ -fPIC" .. && make
 	python3 setup.py develop
 
 test: build

diff --git a/pyspoa.cpp b/pyspoa.cpp
@@ -2,29 +2,25 @@
 #include <pybind11/stl.h>
 #include <pybind11/pybind11.h>
 
-using namespace std;
-using namespace spoa;
-using namespace pybind11;
-using namespace pybind11::literals;
+using namespace pybind11::literals;  // for _a in pybind def
 
-
-auto poa(vector<string> sequences, int algorithm, bool genmsa,
+auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
 	 int m, int n, int g, int e, int q, int c) -> pybind11::tuple
 {
-    auto alignment_engine = createAlignmentEngine(
-       static_cast<AlignmentType>(algorithm), m, n, g, e, q, c
-    );
+    auto alignment_engine = spoa::AlignmentEngine::Create(
+       spoa::AlignmentType::kSW, m, n, g, e, q, c);
 
-    auto graph = createGraph();
+    spoa::Graph graph{};
 
     for (const auto& it: sequences) {
-	auto alignment = alignment_engine->align(it, graph);
-	graph->add_alignment(alignment, it);
+	    auto alignment = alignment_engine->Align(it, graph);
+	    graph.AddAlignment(alignment, it);
     }
 
-    string consensus = graph->generate_consensus();
-    vector<string> msa;
-    if (genmsa) graph->generate_multiple_sequence_alignment(msa);
+    auto consensus = graph.GenerateConsensus();
+    std::vector<std::string> msa;
+    if (genmsa)
+        msa = graph.GenerateMultipleSequenceAlignment();
     return pybind11::make_tuple(consensus, msa);
 }
 

diff --git a/setup.py b/setup.py
@@ -90,6 +90,7 @@ def build_extensions(self):
         ['pyspoa.cpp'],
         include_dirs=[
             'src/include/spoa',
+            'src/vendor/cereal/include',
             get_pybind_include(),
             get_pybind_include(user=True),
         ],
@@ -108,7 +109,7 @@ def build_extensions(self):
 
 setup(
     name='pyspoa',
-    version='0.0.2',
+    version='0.0.3',
     author='Oxford Nanoporetech Technologies, Ltd.',
     author_email='[email protected]',
     url='https://github.com/nanoporetech/pyspoa',

diff --git a/src b/src
+10 −3		.gitmodules
+41 −31		.travis.yml
+135 −66		CMakeLists.txt
+116 −124		README.md
+73 −52		include/spoa/alignment_engine.hpp
+17 −0		include/spoa/architectures.hpp
+240 −137		include/spoa/graph.hpp
+5 −6		include/spoa/spoa.hpp
+82 −63		src/alignment_engine.cpp
+48 −0		src/dispatcher.cpp
+571 −654		src/graph.cpp
+299 −163		src/main.cpp
+0 −24		src/sequence.cpp
+0 −57		src/sequence.hpp
+0 −1,972		src/simd_alignment_engine.cpp
+100 −55		src/simd_alignment_engine.hpp
+17 −0		src/simd_alignment_engine_dispatch.cpp
+2,062 −0		src/simd_alignment_engine_implementation.hpp
+805 −820		src/sisd_alignment_engine.cpp
+71 −52		src/sisd_alignment_engine.hpp
+0 −220		test/data/sample.fastq
+ −		test/data/sample.fastq.gz
+311 −786		test/spoa_test.cpp
+0 −9		test/spoa_test_config.h.in
+1 −1		vendor/bioparser
+1 −0		vendor/cereal
+1 −0		vendor/cpu_features
+0 −1		vendor/googletest
+1 −0		vendor/simde