Added 64-bit version of divsufsort.

4 files changed, 31 insertions, 14 deletions

diff --git a/lib/CMakeLists.txt b/lib/CMakeLists.txt
index cbcb427..56e7942 100644
--- a/lib/CMakeLists.txt
+++ b/lib/CMakeLists.txt
@@ -1,8 +1,10 @@
 include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
                     "${CMAKE_CURRENT_BINARY_DIR}/../include")
 
+set(divsufsort_SRCS divsufsort.c sssort.c trsort.c utils.c)
+
 ## libdivsufsort ##
-add_library(divsufsort divsufsort.c sssort.c trsort.c utils.c)
+add_library(divsufsort ${divsufsort_SRCS})
 install(TARGETS divsufsort
   RUNTIME DESTINATION bin
   LIBRARY DESTINATION lib
@@ -12,3 +14,18 @@ set_target_properties(divsufsort PROPERTIES
   SOVERSION "${LIBRARY_VERSION_MAJOR}"
   DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
   RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
+
+## libdivsufsort64 ##
+if(BUILD_DIVSUFSORT64)
+  add_library(divsufsort64 ${divsufsort_SRCS})
+  install(TARGETS divsufsort64
+    RUNTIME DESTINATION bin
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib)
+  set_target_properties(divsufsort64 PROPERTIES
+    VERSION   "${LIBRARY_VERSION_FULL}"
+    SOVERSION "${LIBRARY_VERSION_MAJOR}"
+    DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
+    COMPILE_FLAGS "-DBUILD_DIVSUFSORT64"
+    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
+endif(BUILD_DIVSUFSORT64)
diff --git a/lib/divsufsort.c b/lib/divsufsort.c
index 568803f..85c3c43 100644
--- a/lib/divsufsort.c
+++ b/lib/divsufsort.c
@@ -340,8 +340,8 @@ divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) {
   else if(n == 1) { SA[0] = 0; return 0; }
   else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
 
-  bucket_A = malloc(BUCKET_A_SIZE * sizeof(saidx_t));
-  bucket_B = malloc(BUCKET_B_SIZE * sizeof(saidx_t));
+  bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
+  bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
 
   /* Suffixsort. */
   if((bucket_A != NULL) && (bucket_B != NULL)) {
@@ -367,9 +367,9 @@ divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
   if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
   else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
 
-  if((B = A) == NULL) { B = malloc((n + 1) * sizeof(saidx_t)); }
-  bucket_A = malloc(BUCKET_A_SIZE * sizeof(saidx_t));
-  bucket_B = malloc(BUCKET_B_SIZE * sizeof(saidx_t));
+  if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
+  bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
+  bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
 
   /* Burrows-Wheeler Transform. */
   if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
diff --git a/lib/trsort.c b/lib/trsort.c
index 4ec6a17..6fe3e67 100644
--- a/lib/trsort.c
+++ b/lib/trsort.c
@@ -44,19 +44,19 @@ static INLINE
 saint_t
 tr_ilg(saidx_t n) {
 #if defined(BUILD_DIVSUFSORT64)
-  return (n & 0xffffffff00000000) ?
-          ((n & 0xffff000000000000) ?
-            ((n & 0xff00000000000000) ?
+  return (n >> 32) ?
+          ((n >> 48) ?
+            ((n >> 56) ?
               56 + lg_table[(n >> 56) & 0xff] :
               48 + lg_table[(n >> 48) & 0xff]) :
-            ((n & 0x0000ff0000000000) ?
+            ((n >> 40) ?
               40 + lg_table[(n >> 40) & 0xff] :
               32 + lg_table[(n >> 32) & 0xff])) :
-          ((n & 0x00000000ffff0000) ?
-            ((n & 0x00000000ff000000) ?
+          ((n & 0xffff0000) ?
+            ((n & 0xff000000) ?
               24 + lg_table[(n >> 24) & 0xff] :
               16 + lg_table[(n >> 16) & 0xff]) :
-            ((n & 0x000000000000ff00) ?
+            ((n & 0x0000ff00) ?
                8 + lg_table[(n >>  8) & 0xff] :
                0 + lg_table[(n >>  0) & 0xff]));
 #else
diff --git a/lib/utils.c b/lib/utils.c
index 75bd274..90fb23e 100644
--- a/lib/utils.c
+++ b/lib/utils.c
@@ -126,7 +126,7 @@ inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
 
   if((B = A) == NULL) {
     /* Allocate n*sizeof(saidx_t) bytes of memory. */
-    if((B = malloc(n * sizeof(saidx_t))) == NULL) { return -2; }
+    if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
   }
 
   /* Inverse BW transform. */