TravisWheelerLab · Sawwave · Feb 16, 2024 · Feb 16, 2024 · Feb 16, 2024 · Feb 16, 2024
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -108,27 +108,43 @@ add_custom_command(
             $<TARGET_FILE_DIR:awfmindex_static>
 )
 
+# Set common compiler options
 target_compile_options(
-        awfmindex_static
-        PRIVATE
-        -mtune=native
-        -march=native
-        -mavx2
-        -Wall
-        -Wextra
-        ${OpenMP_C_FLAGS}
+    awfmindex_static
+    PRIVATE
+    -mtune=native
+    -march=native
+    -Wall
+    -Wextra
+    ${OpenMP_C_FLAGS}
 )
 
 target_compile_options(
-        awfmindex
-        PRIVATE
-        -mtune=native
-        -march=native
-        -mavx2 
-        -Wall
-        -Wextra
-        ${OpenMP_C_FLAGS}
-)
+    awfmindex
+    PRIVATE
+    -mtune=native
+    -march=native
+    -Wall
+    -Wextra
+    ${OpenMP_C_FLAGS}
+)
+
+# Check if the target architecture is x86_64 (Intel) or aarch64 (ARM)
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64")
+    # Check if the compiler supports AVX2
+    include(CheckCCompilerFlag)
+    CHECK_C_COMPILER_FLAG("-mavx2" COMPILER_SUPPORTS_AVX2)
+
+    if(COMPILER_SUPPORTS_AVX2)
+        # Set AVX2 flags for x86_64 (Intel)
+        target_compile_options(awfmindex_static PRIVATE -mavx2)
+        target_compile_options(awfmindex PRIVATE -mavx2)
+    endif()
+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64")
+    # Set NEON flags for ARM
+    target_compile_options(awfmindex_static PRIVATE -march=armv8-a+simd)
+    target_compile_options(awfmindex PRIVATE -march=armv8-a+simd)
+endif()
 
 install(
         TARGETS awfmindex awfmindex_static

diff --git a/README.md b/README.md
@@ -34,23 +34,37 @@ it manually for either the CMake or legacy Make builds.
 
 ```
 git clone https://github.com/TravisWheelerLab/AvxWindowFmIndex.git
-git submodule init
-git submodule update
+git submodule update --init --recursive --remote
 ```
 
 Now the project is ready to build.
 
 ## CMake Build
 
 The default way to build AwFmIndex is to use CMake. The usual CMake incantations
-will work. This will result in both shared and static libraries written to the
+will work. This will result in both shared libraries written to the
 `build/` directory.
 
 ```
 cmake .
 make
 ```
 
+to instead make static libraries, set the BUILD_SHARED_LIBS variable as follows:
+```
+cmake -DBUILD_SHARED_LIBS=OFF .
+make
+```
+
+
+If you want both, it's eas easy as running both back-to-back
+```
+cmake -DBUILD_SHARED_LIBS=OFF .
+make
+cmake -DBUILD_SHARED_LIBS=ON .
+make
+```
+
 To install on MacOS, you will need to specify the install location of your
 GCC compiler. An Example is given below:
 

diff --git a/test/README.md b/test/README.md
@@ -1,6 +1,4 @@
-These tests are mostly stand-alone, and do not require the AwFmIndex library to be installed. However, some of these tests require libdivsufsort64 to be installed in a find-able location. Before running these tests, install libdivsufsort64 as a shared library in a manner consistent with the library's readme. Note that the 64-bit version is required, and so the cmake call requires the DBUILD_DIVSUFSORT64 flag to be set:
-
+These tests require that the project be built for static libraries. Nothing needs to be installed for these to function. To build the static libraries, cd into the project's home directory and run
 '''
-cd build
-cmake -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_BUILD_TYPE="Release" -DUSE_OPENMP="ON" -DBUILD_SHARED_LIBS="ON" -DBUILD_DIVSUFSORT64:BOOL=ON  .. && make
+cmake -DBUILD_SHARED_LIBS="OFF" . && make
 '''
diff --git a/test/backtraceTest/backtraceTest.c b/test/backtraceTest/backtraceTest.c
@@ -5,8 +5,8 @@
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
-#include "../../lib/FastaVector/src/FastaVector.h"
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/FastaVector.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/backtraceTest/makefile b/test/backtraceTest/makefile
@@ -1,13 +1,15 @@
 TEST_SRC = backtraceTest.c
 SRC = $(wildcard ../../src/*.c)
 
+
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDFLAGS = -L../../build
+LDLIBS = -lfastavector_static -ldivsufsort64
 
 EXE = backtraceTest.out
 
 backtraceTest: $(SRC)
-	gcc $(TEST_SRC) $(SRC) -o $(EXE) $(CFLAGS) $(LDLIBS)
+	gcc $(TEST_SRC) $(SRC) -o $(EXE) $(CFLAGS) $(LDFLAGS) $(LDLIBS)
 
 .PHONY: clean
 clean:

diff --git a/test/bwtTest/bwtTest.c b/test/bwtTest/bwtTest.c
@@ -7,7 +7,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/bwtTest/makefile b/test/bwtTest/makefile
@@ -2,7 +2,7 @@ TEST_SRC = bwtTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = bwtTest.out
 

diff --git a/test/createTests/AwFmCreationTest.c b/test/createTests/AwFmCreationTest.c
@@ -7,7 +7,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/createTests/makefile b/test/createTests/makefile
@@ -2,7 +2,7 @@ TEST_SRC = AwFmCreationTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = createTest.out
 

diff --git a/test/fileTests/AwFmFileTests.c b/test/fileTests/AwFmFileTests.c
@@ -6,7 +6,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/fileTests/makefile b/test/fileTests/makefile
@@ -2,7 +2,7 @@ TEST_SRC = AwFmFileTests.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = fileTests.out
 

diff --git a/test/inMemorySaTest/inMemorySaTest.c b/test/inMemorySaTest/inMemorySaTest.c
@@ -6,7 +6,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/inMemorySaTest/makefile b/test/inMemorySaTest/makefile
@@ -2,7 +2,7 @@ TEST_SRC = inMemorySaTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = saInMemTest.out
 

diff --git a/test/kmerSeedTableTests/kmerSeedTableTests.c b/test/kmerSeedTableTests/kmerSeedTableTests.c
@@ -7,7 +7,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/kmerSeedTableTests/makefile b/test/kmerSeedTableTests/makefile
@@ -2,7 +2,7 @@ TEST_SRC = kmerSeedTableTests.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O3
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = kmerSeedTableTests.out
 

diff --git a/test/multiSequenceIndexTest/AwFmMultiSequenceTest.c b/test/multiSequenceIndexTest/AwFmMultiSequenceTest.c
@@ -17,7 +17,7 @@
 #include "../../src/AwFmSuffixArray.h"
 #include "../test.h"
 #include "FastaVector.h"
-// #include "../../libdivsufsort/build/include/divsufsort64.h"
+// #include "../../lib/libdivsufsort/include/divsufsort64.h"
 
 
 char buffer[2048];

diff --git a/test/multiSequenceIndexTest/makefile b/test/multiSequenceIndexTest/makefile
@@ -2,7 +2,7 @@ TEST_SRC = AwFmMultiSequenceTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O0 -g
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = multiSequenceTest.out
 

diff --git a/test/occurrenceTests/makefile b/test/occurrenceTests/makefile
@@ -2,7 +2,7 @@ TEST_SRC = occurrenceTests.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O0 -g
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = occurrenceTests.out
 

diff --git a/test/occurrenceTests/occurrenceTests.c b/test/occurrenceTests/occurrenceTests.c
@@ -5,7 +5,7 @@
 #include <stdlib.h>
 #include <time.h>
 
-#include "../../lib/libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"

diff --git a/test/parallelSearch/makefile b/test/parallelSearch/makefile
@@ -2,7 +2,7 @@ TEST_SRC = parallelSearchTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O0 -g
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = parallelSearchTest.out
 

diff --git a/test/parallelSearch/parallelSearchTest.c b/test/parallelSearch/parallelSearchTest.c
@@ -16,7 +16,7 @@
 #include "../../src/AwFmSearch.h"
 #include "../../src/AwFmSuffixArray.h"
 #include "../test.h"
-#include "divsufsort64.h"
+#include "../../build/divsufsort64.h"
 
 char buffer[2048];
 uint8_t aminoLookup[21] = {

diff --git a/test/searchTest/makefile b/test/searchTest/makefile
@@ -1,6 +1,10 @@
 TEST_SRC	= searchTest.c
 SRC 			= $(wildcard ../../src/*.c)
-CFLAGS 	= -std=c11 -fsanitize=address -Wall -mtune=native -g -fopenmp -ldivsufsort64 -lfastavector -mavx2 -L../../lib/libdivsufsort/build/lib
+
+CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O0 -g
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
+
 EXE 		= searchTest.out
+
 bwtTest: $(SRC)
-	gcc $(TEST_SRC) $(SRC) -o $(EXE) $(CFLAGS)
+	gcc $(TEST_SRC) $(SRC) -o $(EXE) $(CFLAGS) $(LDLIBS)
diff --git a/test/searchTest/searchTest.c b/test/searchTest/searchTest.c
@@ -6,7 +6,7 @@
 #include <string.h>
 #include <time.h>
 
-#include "../../libdivsufsort/build/include/divsufsort64.h"
+#include "../../build/divsufsort64.h"
 #include "../../src/AwFmCreate.h"
 #include "../../src/AwFmIndex.h"
 #include "../../src/AwFmIndexStruct.h"
@@ -69,7 +69,7 @@ int main(int argc, char **argv) {
 void generateRandomIndex(struct AwFmIndex **index, uint8_t **sequence, size_t sequenceLength, uint64_t **suffixArray) {
 	printf("generating random index.\n");
 	// decide if we're building a nucleotide or amino index.
-	enum AwFmAlphabetType alphabetType	 = (rand() & 1) ? AwFmAlphabetNucleotide : AwFmAlphabetAmino;
+	enum AwFmAlphabetType alphabetType	 = (rand() & 1) ? AwFmAlphabetDna : AwFmAlphabetAmino;
 	struct AwFmIndexConfiguration config = {.suffixArrayCompressionRatio = 200,
 			.kmerLengthInSeedTable																					 = 4,
 			.alphabetType																										 = alphabetType,
@@ -90,7 +90,7 @@ void generateRandomIndex(struct AwFmIndex **index, uint8_t **sequence, size_t se
 		exit(-2);
 	}
 
-	uint8_t *characterLookupTable = alphabetType == AwFmAlphabetNucleotide ? nucleotideLookup : aminoLookup;
+	uint8_t *characterLookupTable = alphabetType == AwFmAlphabetDna ? nucleotideLookup : aminoLookup;
 	uint8_t alphabetCardinalty		= awFmGetAlphabetCardinality(alphabetType);
 	for(size_t i = 0; i < sequenceLength; i++) {
 		uint8_t characterIndex = rand() % (alphabetCardinalty + 1);	 //+1 is for ambiguity character
@@ -121,7 +121,7 @@ void testSearchForRandomKmers(
 		// build the kmer.
 		// printf("nuclookup ptr %p, amino %p, index p: %p\n", nucleotideLookup, aminoLookup, index);
 		uint8_t *characterLookupTable =
-				(index->config.alphabetType == AwFmAlphabetNucleotide) ? &nucleotideLookup[0] : &aminoLookup[0];
+				(index->config.alphabetType == AwFmAlphabetDna) ? &nucleotideLookup[0] : &aminoLookup[0];
 		uint8_t alphabetCardinalty = awFmGetAlphabetCardinality(index->config.alphabetType);
 		for(size_t i = 0; i < kmerLength; i++) {
 			kmer[i] = characterLookupTable[rand() % alphabetCardinalty];
@@ -181,5 +181,5 @@ void testRangeForCorrectness(const struct AwFmSearchRange *range, const uint8_t
 
 struct AwFmSearchRange findRangeForKmer(
 		const struct AwFmIndex *_RESTRICT_ const index, const char *kmer, const uint64_t kmerLength) {
-	return awFmDatabaseSingleKmerExactMatch(index, kmer, kmerLength);
+	return awFmFindSearchRangeForString(index, kmer, kmerLength);
 }
diff --git a/test/suffixArrayCompressionTests/makefile b/test/suffixArrayCompressionTests/makefile
@@ -2,7 +2,7 @@ TEST_SRC = saTest.c
 SRC = $(wildcard ../../src/*.c)
 
 CFLAGS = -std=c11 -fsanitize=address -Wall -mtune=native -fopenmp -mavx2 -O0 -g
-LDLIBS = ../../lib/FastaVector/build/libfastavector_static.a ../../lib/libdivsufsort/build/lib/libdivsufsort64.a
+LDLIBS = ../../build/libfastavector_static.a ../../build/libdivsufsort64.a
 
 EXE = saTest.out