Merge pull request #4505 from vgteam/faster-gaf-sorting

Faster GAF sorting
vgteam · Jan 26, 2025 · c740ed6 · c740ed6 · adamnovak · Jan 26, 2025
2 parents a1dc9e0 + 0a53f54
commit c740ed6
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Showing 11 changed files with 1,794 additions and 241 deletions.
diff --git a/Makefile b/Makefile
@@ -537,7 +537,7 @@ test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BI
 
 # Somebody has been polluting the test directory with temporary files that are not deleted after the tests.
 # To make git status more useful, we delete everything that looks like a temporary file.
-clean-test:
+clean-tests:
 	cd test && rm -rf tmp && mkdir tmp && mv 2_2.mat build_graph.cpp default.mat tmp && rm -f *.* && mv tmp/* . && rmdir tmp
 
 docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(ALGORITHMS_SRC_DIR)/*.cpp $(ALGORITHMS_SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp

diff --git a/deps/gbwt b/deps/gbwt
diff --git a/deps/gbwtgraph b/deps/gbwtgraph
+1 −1		LICENSE
+1 −1		README.md
+5 −1		include/gbwt/support.h
+37 −2		src/support.cpp
+89 −0		tests/test_support.cpp
+0 −1		include/gbwtgraph/index.h
+3 −7		include/gbwtgraph/utils.h
+9 −16		src/gbwtgraph.cpp