Update submodule spoa

lbcb-sci · Sep 18, 2019 · 7106b64 · 7106b64
1 parent 95e9a63
commit 7106b64
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/window.cpp b/src/window.cpp
@@ -87,14 +87,14 @@ bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment
         spoa::Alignment alignment;
         if (positions_[i].first < offset && positions_[i].second >
             sequences_.front().second - offset) {
-            alignment = alignment_engine->align_sequence_with_graph(
-                sequences_[i].first, sequences_[i].second, graph);
+            alignment = alignment_engine->align(sequences_[i].first,
+                sequences_[i].second, graph);
         } else {
             std::vector<int32_t> mapping;
             auto subgraph = graph->subgraph(positions_[i].first,
                 positions_[i].second, mapping);
-            alignment = alignment_engine->align_sequence_with_graph(
-                sequences_[i].first, sequences_[i].second, subgraph);
+            alignment = alignment_engine->align( sequences_[i].first,
+                sequences_[i].second, subgraph);
             subgraph->update_alignment(alignment, mapping);
         }
 

diff --git a/vendor/spoa b/vendor/spoa
+2 −0		.travis.yml
+12 −5		CMakeLists.txt
+59 −36		README.md
+34 −14		include/spoa/alignment_engine.hpp
+65 −54		include/spoa/graph.hpp
+47 −23		src/alignment_engine.cpp
+144 −123		src/graph.cpp
+105 −71		src/main.cpp
+5 −4		src/sequence.cpp
+6 −7		src/sequence.hpp
+1,328 −232		src/simd_alignment_engine.cpp
+28 −15		src/simd_alignment_engine.hpp
+727 −127		src/sisd_alignment_engine.cpp
+25 −14		src/sisd_alignment_engine.hpp
+579 −29		test/spoa_test.cpp
+1 −1		vendor/bioparser
+1 −1		vendor/googletest