New version: more memory-efficient etc.

CMakeLists.txt

@@ -5,7 +5,19 @@ project(Nexus)
 # add pop count, c++ version and compiler warnings
 add_compile_options(-mpopcnt -std=gnu++14 -Wall -pedantic)
 
-add_library(AuxiliaryClasses src/range.cpp src/fmindex.cpp src/nucleotide.cpp src/searchstrategy.cpp src/buildIndexAuxiliary.cpp src/fmpos.cpp src/fmocc.cpp src/search.cpp src/fmindexDBG.cpp src/strainfreemapper.cpp)
+include_directories("${PROJECT_SOURCE_DIR}/radixSA64/")
+
+include_directories("${PROJECT_SOURCE_DIR}/longestcommonprefix/")
+
+include_directories("${PROJECT_SOURCE_DIR}/libdivsufsort/include/")
+find_library(SA_LIB NAMES divsufsort64 libdivsufsort64 libdivsufsort64.so PATHS "${PROJECT_SOURCE_DIR}/libdivsufsort/lib" "${PROJECT_SOURCE_DIR}/libdivsufsort" NO_DEFAULT_PATH REQUIRED)
+if(NOT SA_LIB)
+  message(FATAL_ERROR "divsufsort64 library not found")
+endif()
+
+add_library(AuxiliaryClasses src/range.cpp src/fmindex.cpp src/nucleotide.cpp src/searchstrategy.cpp src/buildIndexAuxiliary.cpp src/fmpos.cpp src/fmocc.cpp src/search.cpp src/fmindexDBG.cpp src/strainfreemapper.cpp longestcommonprefix/longestCommonPrefix.cpp)
+
+target_link_libraries(AuxiliaryClasses "${SA_LIB}" )
 
 #add_compile_definitions(ALPHABET=6)
 add_definitions(-DALPHABET=6)
@@ -16,6 +28,9 @@ target_link_libraries(columba AuxiliaryClasses )
 add_executable(nexus src/mainDBG.cpp src/benchmarking.cpp)
 target_link_libraries(nexus AuxiliaryClasses )
 
+add_executable(nexusStats src/mainstats.cpp)
+target_link_libraries(nexusStats AuxiliaryClasses )
+
 add_executable(nexusBuild src/buildDBG.cpp)
 target_link_libraries(nexusBuild AuxiliaryClasses )
 

libdivsufsort/include/config.h

@@ -0,0 +1,81 @@
+/*
+ * config.h for libdivsufsort
+ * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef _CONFIG_H
+#define _CONFIG_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/** Define to the version of this package. **/
+#define PROJECT_VERSION_FULL "2.0.1-14-g5f60d6f"
+
+/** Define to 1 if you have the header files. **/
+#define HAVE_INTTYPES_H 1
+#define HAVE_STDDEF_H 1
+#define HAVE_STDINT_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_SYS_TYPES_H 1
+
+/** for WinIO **/
+/* #undef HAVE_IO_H */
+/* #undef HAVE_FCNTL_H */
+/* #undef HAVE__SETMODE */
+/* #undef HAVE_SETMODE */
+/* #undef HAVE__FILENO */
+/* #undef HAVE_FOPEN_S */
+/* #undef HAVE__O_BINARY */
+#ifndef HAVE__SETMODE
+# if HAVE_SETMODE
+#  define _setmode setmode
+#  define HAVE__SETMODE 1
+# endif
+# if HAVE__SETMODE && !HAVE__O_BINARY
+#  define _O_BINARY 0
+#  define HAVE__O_BINARY 1
+# endif
+#endif
+
+/** for inline **/
+#ifndef INLINE
+# define INLINE inline
+#endif
+
+/** for VC++ warning **/
+#ifdef _MSC_VER
+#pragma warning(disable: 4127)
+#endif
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _CONFIG_H */

libdivsufsort/include/divsufsort.h

@@ -0,0 +1,180 @@
+/*
+ * divsufsort.h for libdivsufsort
+ * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef _DIVSUFSORT_H
+#define _DIVSUFSORT_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include <inttypes.h>
+
+#ifndef DIVSUFSORT_API
+# ifdef DIVSUFSORT_BUILD_DLL
+#  define DIVSUFSORT_API 
+# else
+#  define DIVSUFSORT_API 
+# endif
+#endif
+
+/*- Datatypes -*/
+#ifndef SAUCHAR_T
+#define SAUCHAR_T
+typedef uint8_t sauchar_t;
+#endif /* SAUCHAR_T */
+#ifndef SAINT_T
+#define SAINT_T
+typedef int32_t saint_t;
+#endif /* SAINT_T */
+#ifndef SAIDX_T
+#define SAIDX_T
+typedef int32_t saidx_t;
+#endif /* SAIDX_T */
+#ifndef PRIdSAINT_T
+#define PRIdSAINT_T PRId32
+#endif /* PRIdSAINT_T */
+#ifndef PRIdSAIDX_T
+#define PRIdSAIDX_T PRId32
+#endif /* PRIdSAIDX_T */
+
+
+/*- Prototypes -*/
+
+/**
+ * Constructs the suffix array of a given string.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The output array of suffixes.
+ * @param n The length of the given string.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n);
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @return The primary index if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n);
+
+/**
+ * Returns the version of the divsufsort library.
+ * @return The version number string.
+ */
+DIVSUFSORT_API
+const char *
+divsufsort_version(void);
+
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string and suffix array.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param SA[0..n-1] The suffix array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The output primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+bw_transform(const sauchar_t *T, sauchar_t *U,
+             saidx_t *SA /* can NULL */,
+             saidx_t n, saidx_t *idx);
+
+/**
+ * Inverse BW-transforms a given BWTed string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+inverse_bw_transform(const sauchar_t *T, sauchar_t *U,
+                     saidx_t *A /* can NULL */,
+                     saidx_t n, saidx_t idx);
+
+/**
+ * Checks the correctness of a given suffix array.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The input suffix array.
+ * @param n The length of the given string.
+ * @param verbose The verbose mode.
+ * @return 0 if no error occurred.
+ */
+DIVSUFSORT_API
+saint_t
+sufcheck(const sauchar_t *T, const saidx_t *SA, saidx_t n, saint_t verbose);
+
+/**
+ * Search for the pattern P in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param P[0..Psize-1] The input pattern string.
+ * @param Psize The length of the given pattern string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+sa_search(const sauchar_t *T, saidx_t Tsize,
+          const sauchar_t *P, saidx_t Psize,
+          const saidx_t *SA, saidx_t SAsize,
+          saidx_t *left);
+
+/**
+ * Search for the character c in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param c The input character.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
+                const saidx_t *SA, saidx_t SAsize,
+                saint_t c, saidx_t *left);
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _DIVSUFSORT_H */