pythonffi: fix missing WfaVariant

pjotrp · pjotrp · commit 986001cc7ee0 · 2023-02-10T14:40:55.000-06:00
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -43,6 +43,8 @@ option(WFA_GITMODULE "Force local git submodule for WFA2LIB" ON) # disable in di
 include(CheckIPOSupported) # adds lto
 check_ipo_supported(RESULT ipo_supported OUTPUT output)
 
+set(EXTRA_FLAGS " ") # otherwise it injects OFF
+
 # ---- Dependencies
 
 if(OPENMP)
@@ -463,6 +465,7 @@ install(TARGETS pyvcflib LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
 
 enable_testing()
 
+
 function(add_pytest TEST_FILE)
   add_test(
       NAME ${TEST_FILE}
diff --git a/contrib/WFA2-lib b/contrib/WFA2-lib
@@ -1 +1 @@
-Subproject commit 188b522ae634add3c692ca7547595b7266f1fa19
+Subproject commit ab690aa9b3015dc2551387080cbc067d6ab4e490
diff --git a/src/pythonffi.cpp b/src/pythonffi.cpp
@@ -60,8 +60,12 @@ PYBIND11_MODULE(pyvcflib, m)
       .def_readonly("sampleNames", &Variant::sampleNames)
       .def_readonly("samples", &Variant::samples)
       .def("legacy_parsedAlternates", &Variant::legacy_parsedAlternates)
-      // .def("parsedAlternates", &WfaVariant::parsedAlternates)
       ;
+
+  py::class_<WfaVariant, Variant>(m, "WfaVariant", "WFA VCF record")
+      .def(py::init<VariantCallFile &>() )
+      .def("parsedAlternates", &WfaVariant::parsedAlternates);
+
   py::class_<VariantCallFile>(m, "VariantCallFile", "VCF file")
       .def(py::init())
       .def("openFile",&VariantCallFile::openFile,"Open the VCF")
diff --git a/test/tests/realign.py b/test/tests/realign.py
@@ -48,7 +48,7 @@ def test_sw_wf_compare(self):
     def test_wfbug2(self):
         vcf = VariantCallFile()
         vcf.openFile("../samples/10134514.vcf")
-        var = Variant(vcf)
+        var = WfaVariant(vcf)
         vcf.getNextVariant(var)
         self.assertEqual(var.name,"grch38#chr4_10083863-10181258.vcf:grch38#chr4")
         self.assertEqual(var.ref,'GGAGAATCCCAATTGATGG')
