Merge branch 'update-spoa' into 'dev'

Update spoa and add `min_coverage` param See merge request epi2melabs/pyspoa!3
nanoporetech · Oct 2, 2023 · ec00b28 · ec00b28
2 parents d651967 + e6c9c8e
commit ec00b28
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Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.2.0]
+### Changed
+- Updated SPOA to v4.1.2
+### Added
+- `min_coverage` option recently introduced in SPOA
+
 ## [v0.1.0]
 ### Changed
 - Moved CI to internal infrastructure

diff --git a/pyspoa.cpp b/pyspoa.cpp
@@ -5,7 +5,7 @@
 using namespace pybind11::literals;  // for _a in pybind def
 
 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
+	 int m, int n, int g, int e, int q, int c, int min_coverage) -> pybind11::tuple
 {
     auto alignment_engine = spoa::AlignmentEngine::Create(
       static_cast<spoa::AlignmentType>(algorithm), m, n, g, e, q, c
@@ -18,7 +18,7 @@ auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
 	    graph.AddAlignment(alignment, it);
     }
 
-    auto consensus = graph.GenerateConsensus();
+    auto consensus = graph.GenerateConsensus(min_coverage);
     std::vector<std::string> msa;
     if (genmsa)
         msa = graph.GenerateMultipleSequenceAlignment();
@@ -30,7 +30,8 @@ PYBIND11_MODULE(spoa, m) {
     m.def(
        "poa", &poa, "",
        "sequences"_a, "algorithm"_a=0, "genmsa"_a=true,
-       "m"_a=5, "n"_a=-4, "g"_a=-8, "e"_a=-6, "q"_a=-10, "c"_a=-4
+       "m"_a=5, "n"_a=-4, "g"_a=-8, "e"_a=-6, "q"_a=-10, "c"_a=-4,
+       "min_coverage"_a=-1
     );
 
     m.attr("__version__") = VERSION_INFO;

diff --git a/setup.py b/setup.py
@@ -139,7 +139,7 @@ def build_extensions(self):
 
 setup(
     name='pyspoa',
-    version='0.1.0',
+    version='0.2.0',
     author='Oxford Nanoporetech Technologies, Ltd.',
     author_email='support@nanoporetech.com',
     url='https://github.com/nanoporetech/pyspoa',

diff --git a/src b/src
+29 −14		.github/workflows/spoa.yml
+3 −0		.gitignore
+18 −20		CMakeLists.txt
+53 −47		README.md
+18 −0		include/meson.build
+2 −0		include/spoa/graph.hpp
+1 −0		include/spoa/spoa.hpp
+14 −0		include/spoa/version.hpp
+111 −0		meson.build
+56 −0		meson_options.txt
+0 −0		src/architectures.hpp
+11 −0		src/graph.cpp
+9 −2		src/main.cpp
+68 −0		src/meson.build
+1 −1		src/simd_alignment_engine.hpp
+75 −4		src/simd_alignment_engine_dispatcher.cpp
+50 −120		src/simd_alignment_engine_implementation.hpp
+12 −0		src/spoa_config.h.in
+13 −0		src/version.cpp
+5 −0		subprojects/bioparser.wrap
+5 −0		subprojects/biosoup.wrap
+15 −0		subprojects/cereal.wrap
+16 −0		subprojects/gtest.wrap
+9 −0		subprojects/simde.wrap
+31 −0		test/meson.build
+24 −29		test/spoa_test.cpp
+14 −0		test/spoa_test_config.h.in