Merge pull request #203 from pangenome/update_abpoa

update SPOA and abPOA
pangenome · Jan 11, 2024 · 620d1d4 · 620d1d4
2 parents ae949a1 + 4b27ce4
commit 620d1d4
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/deps/abPOA b/deps/abPOA
diff --git a/deps/spoa b/deps/spoa
diff --git a/src/breaks.cpp b/src/breaks.cpp
@@ -244,11 +244,11 @@ namespace smoothxg {
                     }
                     // if there is, set the cut length to some fraction of it
                     std::vector<double> lengths;
-                    double max_z = 0;
+                    //double max_z = 0;
                     for (auto& repeat : repeats) {
                         if (repeat.length > 0) {
                             lengths.push_back(repeat.length);
-                            max_z = std::max(repeat.z_score, max_z);
+                            //max_z = std::max(repeat.z_score, max_z);
                         }
                     }
                     found_repeat = !lengths.empty();
+2 −0		.gitignore
+7 −1		CMakeLists.txt
+43 −24		Makefile
+54 −41		README.md
+1 −1		abpoa.pc.in
+ −		pog.png
+1 −2		python/README.md
+4 −4		python/example.py
+52 −41		setup.py
+1 −1		src/abpoa.c
+1 −1		src/abpoa_align.h
+1 −1		src/abpoa_output.c
+2 −2		src/abpoa_seed.c
+15 −14		src/simd_abpoa_align.c
+29 −14		.github/workflows/spoa.yml
+3 −0		.gitignore
+18 −20		CMakeLists.txt
+53 −47		README.md
+18 −0		include/meson.build
+6 −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
+33 −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