Merge branch 'min-coverage-default-None' into 'dev'

None default argument for min_coverage

See merge request epi2melabs/pyspoa!5

CHANGELOG.md

@@ -4,6 +4,10 @@ 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).
 
+## [v0.2.1]
+### Changed
+- Default argument for `min_coverage` to `None`
+
 ## [v0.2.0]
 ### Changed
 - Updated SPOA to v4.1.2

pyspoa.cpp

@@ -1,12 +1,19 @@
 #include "spoa.hpp"
+
+#define PYBIND11_DETAILED_ERROR_MESSAGES  // for type information in casting errors
 #include <pybind11/stl.h>
 #include <pybind11/pybind11.h>
 
 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, int min_coverage) -> pybind11::tuple
+	 int m, int n, int g, int e, int q, int c, pybind11::object min_coverage) -> pybind11::tuple
 {
+    // set min_coverage to the default of the SPOA CLI (-1) if None
+    int min_cov = -1;
+    if (min_coverage != pybind11::none()) {
+        min_cov = min_coverage.cast<int>();
+    }
     auto alignment_engine = spoa::AlignmentEngine::Create(
       static_cast<spoa::AlignmentType>(algorithm), m, n, g, e, q, c
     );
@@ -18,7 +25,7 @@ auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
 	    graph.AddAlignment(alignment, it);
     }
 
-    auto consensus = graph.GenerateConsensus(min_coverage);
+    auto consensus = graph.GenerateConsensus(min_cov);
     std::vector<std::string> msa;
     if (genmsa)
         msa = graph.GenerateMultipleSequenceAlignment();
@@ -31,7 +38,7 @@ PYBIND11_MODULE(spoa, m) {
        "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,
-       "min_coverage"_a=-1
+       "min_coverage"_a=pybind11::none()
     );
 
     m.attr("__version__") = VERSION_INFO;

setup.py

@@ -139,7 +139,7 @@ def build_extensions(self):
 
 setup(
     name='pyspoa',
-    version='0.2.0',
+    version='0.2.1',
     author='Oxford Nanoporetech Technologies, Ltd.',
     author_email='support@nanoporetech.com',
     url='https://github.com/nanoporetech/pyspoa',

tests/test_pyspoa.py

@@ -18,6 +18,30 @@ def test_bindings_no_msa(self):
         self.assertEqual(consensus, 'AACTTATA')
         self.assertEqual(len(msa), 0)
 
+    def test_bindings_min_coverage(self):
+        """ simple poa to check bindings with `min_coverage` param"""
+        consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'], min_coverage=3)
+        self.assertEqual(consensus, 'AACTAT')
+        self.assertEqual(len(msa), 3)
+
+    def test_bindings_min_coverage_None(self):
+        """ simple poa to check bindings with `min_coverage=None`"""
+        consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'], min_coverage=None)
+        self.assertEqual(consensus, 'AACTTATA')
+        self.assertEqual(len(msa), 3)
+
+    def test_bindings_min_coverage_wrong_type_string(self):
+        """ check that bindings with `min_coverage=str` throw error"""
+        self.assertRaises(
+            RuntimeError, poa, ["AACTTATA", "AACTTATG", "AACTATA"], min_coverage="x"
+        )
+
+    def test_bindings_min_coverage_wrong_type_float(self):
+        """ check that bindings with `min_coverage=float` throw error"""
+        self.assertRaises(
+            RuntimeError, poa, ["AACTTATA", "AACTTATG", "AACTATA"], min_coverage=1.5
+        )
+
 
 if __name__ == '__main__':
     main()