Implemented suffix array construction of a long 16-bit array (libsais16x64).

Author: IlyaGrebnov

CHANGES

@@ -1,5 +1,8 @@
+Changes in 2.8.3 (June 11, 2024)
+- Implemented suffix array construction of a long 16-bit array (libsais16x64).
+
 Changes in 2.8.2 (May 27, 2024)
-- Implemented suffix array construction of a long integer array (libsais64).
+- Implemented suffix array construction of a long 64-bit array (libsais64).
 
 Changes in 2.8.1 (April 5, 2024)
 - Fixed out-of-bound memory access issue for large inputs (libsais64).

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.10)
 
-project(libsais VERSION 2.8.2 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
+project(libsais VERSION 2.8.3 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
 
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_C_STANDARD_REQUIRED ON)
@@ -20,9 +20,11 @@ add_library(libsais ${LIBSAIS_LIBRARY_TYPE})
 target_sources(libsais PRIVATE
     include/libsais.h
     include/libsais16.h
+    include/libsais16x64.h
     include/libsais64.h
     src/libsais.c
     src/libsais16.c
+    src/libsais16x64.c
     src/libsais64.c
 )
 

README.md

@@ -23,8 +23,10 @@ The libsais provides simple C99 API to construct suffix array and Burrows-Wheele
 The libsais is released under the [Apache License Version 2.0](LICENSE "Apache license")
 
 ## Changes
+* June 11, 2024 (2.8.3)
+  * Implemented suffix array construction of a long 16-bit array (libsais16x64).
 * May 27, 2024 (2.8.2)
-  * Implemented suffix array construction of a long integer array (libsais64).
+  * Implemented suffix array construction of a long 64-bit array (libsais64).
 * April 5, 2024 (2.8.1)
   * Fixed out-of-bound memory access issue for large inputs (libsais64).
 * March 3, 2024 (2.8.0)
@@ -65,11 +67,12 @@ The libsais is released under the [Apache License Version 2.0](LICENSE "Apache l
 
 ## Versions of the libsais
 * [libsais.c](src/libsais.c) (and corresponding [libsais.h](include/libsais.h)) is for suffix array, PLCP, LCP, forward BWT and reverse BWT construction over 8-bit inputs smaller than 2GB (2147483648 bytes).
-  * This version of the library could also be used to construct suffix array of an integer array (with a caveat that input array must be mutable).
-* [libsais64.c](src/libsais64.c) (and corresponding [libsais64.h](include/libsais64.h)) is optional extension of the library for inputs larger or equlas to 2GB (2147483648 bytes).
-* [libsais16.c](src/libsais16.c) (and corresponding [libsais16.h](include/libsais16.h)) is independent version of the library for 16-bit inputs.
+  * [libsais64.c](src/libsais64.c) (and corresponding [libsais64.h](include/libsais64.h)) is optional extension of the library for inputs larger or equlas to 2GB (2147483648 bytes).
+  * This versions of the library could also be used to construct suffix array of an integer array (with a caveat that input array must be mutable).
+* [libsais16.c](src/libsais16.c) + [libsais16x64.c](src/libsais16x64.c) (and corresponding [libsais16.h](include/libsais16.h) + [libsais16x64.h](include/libsais16x64.h)) is independent version of the library for 16-bit inputs.
+  * This version of the library could also be used to construct suffix array and BWT of a set of strings by adding a unique end-of-string symbol to each string and then computing the result for the concatenated string.
 
-## Examples of APIs (see [libsais.h](include/libsais.h), [libsais16.h](include/libsais16.h) and [libsais64.h](include/libsais64.h) for complete APIs list)
+## Examples of APIs (see [libsais.h](include/libsais.h), [libsais16.h](include/libsais16.h), [libsais16x64.h](include/libsais16x64.h) and [libsais64.h](include/libsais64.h) for complete APIs list)
 ```c
     /**
     * Constructs the suffix array of a given string.
@@ -124,7 +127,7 @@ The libsais is released under the [Apache License Version 2.0](LICENSE "Apache l
 CPMAddPackage(
   NAME libsais
   GITHUB_REPOSITORY IlyaGrebnov/libsais
-  GIT_TAG v2.8.1
+  GIT_TAG v2.8.3
   OPTIONS
     "LIBSAIS_USE_OPENMP OFF"
     "LIBSAIS_BUILD_SHARED_LIB OFF"

VERSION

@@ -1 +1 @@
-2.8.2
+2.8.3

include/libsais.h

@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS_VERSION_MAJOR   2
 #define LIBSAIS_VERSION_MINOR   8
-#define LIBSAIS_VERSION_PATCH   2
-#define LIBSAIS_VERSION_STRING  "2.8.2"
+#define LIBSAIS_VERSION_PATCH   3
+#define LIBSAIS_VERSION_STRING  "2.8.3"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED

include/libsais16.h

@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS16_VERSION_MAJOR   2
 #define LIBSAIS16_VERSION_MINOR   8
-#define LIBSAIS16_VERSION_PATCH   2
-#define LIBSAIS16_VERSION_STRING  "2.8.2"
+#define LIBSAIS16_VERSION_PATCH   3
+#define LIBSAIS16_VERSION_STRING  "2.8.3"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED
@@ -83,6 +83,18 @@ extern "C" {
     */
     LIBSAIS16_API int32_t libsais16(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
 
+    /**
+    * Constructs the suffix array of a given integer array.
+    * Note, during construction input array will be modified, but restored at the end if no errors occurred.
+    * @param T [0..n-1] The input integer array.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the integer array.
+    * @param k The alphabet size of the input integer array.
+    * @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS16_API int32_t libsais16_int(int32_t * T, int32_t * SA, int32_t n, int32_t k, int32_t fs);
+
     /**
     * Constructs the suffix array of a given 16-bit string using libsais16 context.
     * @param ctx The libsais16 context.
@@ -107,6 +119,19 @@ extern "C" {
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
     LIBSAIS16_API int32_t libsais16_omp(const uint16_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
+
+    /**
+    * Constructs the suffix array of a given integer array in parallel using OpenMP.
+    * Note, during construction input array will be modified, but restored at the end if no errors occurred.
+    * @param T [0..n-1] The input integer array.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the integer array.
+    * @param k The alphabet size of the input integer array.
+    * @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
+    * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS16_API int32_t libsais16_int_omp(int32_t * T, int32_t * SA, int32_t n, int32_t k, int32_t fs, int32_t threads);
 #endif
 
     /**