Rewrote bwt.c.

1 files changed, 138 insertions, 70 deletions

diff --git a/examples/bwt.c b/examples/bwt.c
index 842712d..5a362d0 100644
--- a/examples/bwt.c
+++ b/examples/bwt.c
@@ -24,129 +24,197 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#ifdef HAVE_CONFIG_H
+#if HAVE_CONFIG_H
 # include "config.h"
 #endif
-#include <divsufsort.h>
 #include <stdio.h>
+#if HAVE_STRING_H
+# include <string.h>
+#endif
 #if HAVE_STDLIB_H
 # include <stdlib.h>
 #endif
-#if HAVE_STRING_H
-# if !STDC_HEADERS && HAVE_MEMORY_H
-#  include <memory.h>
-# endif
-# include <string.h>
+#if HAVE_MEMORY_H
+# include <memory.h>
+#endif
+#if HAVE_STDDEF_H
+# include <stddef.h>
 #endif
 #if HAVE_STRINGS_H
 # include <strings.h>
 #endif
+#if HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#if HAVE_IO_H && HAVE_FCNTL_H
+# include <io.h>
+# include <fcntl.h>
+#endif
 #include <time.h>
+#include <divsufsort.h>
+#include "lfs.h"
 
 
 static
-saidx_t
-_str2size(const char *str) {
-  saidx_t s[3];
-  saidx_t t;
-  int i, c;
-  for(i = 0, t = s[0] = s[1] = s[2] = 0; (c = str[i]) != '\0'; ++i) {
-    if(('0' <= c) && (c <= '9')) {
-      t = (t * 10) + (c - '0');
-    } else {
-      switch(c) {
-      case 'm':
-      case 'M':
-        s[0] += t << 20;
-        break;
-      case 'k':
-      case 'K':
-        s[1] += t << 10;
-        break;
-      case 'b':
-      case 'B':
-        s[2] += t;
-        break;
-      }
-      t = 0;
-    }
-  }
-  return s[0] + s[1] + s[2];
+size_t
+write_int(FILE *fp, saidx_t n) {
+  unsigned char c[4];
+  c[0] = (unsigned char)((n >>  0) & 0xff), c[1] = (unsigned char)((n >>  8) & 0xff),
+  c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff);
+  return fwrite(c, sizeof(unsigned char), 4, fp);
+}
+
+static
+void
+print_help(const char *progname, int status) {
+  fprintf(stderr,
+          "bwt, a burrows-wheeler transform program, version %s.\n",
+          divsufsort_version());
+  fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname);
+  fprintf(stderr, "  -b num    set block size to num MiB [1..512] (default: 32)\n\n");
+  exit(status);
 }
 
 int
 main(int argc, const char *argv[]) {
+  FILE *fp, *ofp;
+  const char *fname, *ofname;
   sauchar_t *T;
   saidx_t *SA;
-  saidx_t m, n, blocksize, idx;
+  LFS_OFF_T n;
+  size_t m;
+  saidx_t pidx;
   clock_t start,finish;
+  saint_t i, blocksize = 32, needclose = 3;
 
-  /* Check argument. */
-  if(((argc != 1) && (argc != 2)) ||
-     ((argc == 2) && (strcmp(argv[1], "-h") == 0)) ||
-     ((argc == 2) && (strcmp(argv[1], "--help") == 0))) {
-    fprintf(stderr,
-      "bwt, a burrows-wheeler transform program, version %s.\n"
-      , divsufsort_version());
-    fprintf(stderr,
-      "usage: %s [BLOCKSIZE] < STDIN > STDOUT\n\n"
-      , argv[0]);
-    exit(EXIT_FAILURE);
+  /* Check arguments. */
+  if((argc == 1) ||
+     (strcmp(argv[1], "-h") == 0) ||
+     (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
+  if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); }
+  i = 1;
+  if(argc == 5) {
+    if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); }
+    blocksize = atoi(argv[i + 1]);
+    if(blocksize < 0) { blocksize = 1; }
+    else if(512 < blocksize) { blocksize = 512; }
+    i += 2;
+  }
+  blocksize <<= 20;
+
+  /* Open a file for reading. */
+  if(strcmp(argv[i], "-") != 0) {
+#if HAVE_FOPEN_S
+    if(fopen_s(&fp, fname = argv[i], "rb") != 0) {
+#else
+    if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) {
+#endif
+      fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  } else {
+#if HAVE__SETMODE && HAVE__FILENO
+    if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
+      fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+#endif
+    fp = stdin;
+    fname = "stdin";
+    needclose ^= 1;
   }
-  blocksize = (argc == 2) ? _str2size(argv[1]) : 0;
-  if(blocksize <= 0) {
-    fseek(stdin, 0, SEEK_END);
-    blocksize = ftell(stdin);
-    if(blocksize < 0) { blocksize = BUFSIZ; }
-    rewind(stdin);
+  i += 1;
+
+  /* Open a file for writing. */
+  if(strcmp(argv[i], "-") != 0) {
+#if HAVE_FOPEN_S
+    if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) {
+#else
+    if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) {
+#endif
+      fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  } else {
+#if HAVE__SETMODE && HAVE__FILENO
+    if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
+      fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+#endif
+    ofp = stdout;
+    ofname = "stdout";
+    needclose ^= 2;
   }
 
+  /* Get the file size. */
+  if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
+    n = LFS_FTELL(fp);
+    rewind(fp);
+    if(n < 0) {
+      fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+    if(0x20000000L < n) { n = 0x20000000L; }
+    if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; }
+  } else if(blocksize == 0) { blocksize = 32 << 20; }
+
   /* Allocate 5blocksize bytes of memory. */
-  if(((T = malloc(blocksize * sizeof(sauchar_t))) == NULL) ||
-     ((SA = malloc(blocksize * sizeof(saidx_t))) == NULL)) {
+  T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
+  SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
+  if((T == NULL) || (SA == NULL)) {
     fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
     exit(EXIT_FAILURE);
   }
 
   /* Write the blocksize. */
-  if(fwrite(&blocksize, sizeof(saidx_t), 1, stdout) != 1) {
-    fprintf(stderr, "%s: Cannot write to `stdout': ", argv[0]);
+  if(write_int(ofp, blocksize) != 4) {
+    fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
     perror(NULL);
     exit(EXIT_FAILURE);
   }
 
-  fprintf(stderr, "  BWT (blocksize %d) ... ", (int)blocksize);
-  start=clock();
-  for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, stdin)); n += m) {
+  fprintf(stderr, "  BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
+  start = clock();
+  for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) {
     /* Burrows-Wheeler Transform. */
-    idx = divbwt(T, T, SA, m);
-    if(idx < 0) {
+    pidx = divbwt(T, T, SA, m);
+    if(pidx < 0) {
       fprintf(stderr, "%s (bw_transform): %s.\n",
         argv[0],
-        (idx == -1) ? "Invalid arguments" : "Cannot allocate memory");
+        (pidx == -1) ? "Invalid arguments" : "Cannot allocate memory");
       exit(EXIT_FAILURE);
     }
 
     /* Write the bwted data. */
-    if((fwrite(&idx, sizeof(saidx_t), 1, stdout) != 1) ||
-       (fwrite(T, sizeof(sauchar_t), m, stdout) != m)) {
-      fprintf(stderr, "%s: Cannot write to `stdout': ", argv[0]);
+    if((write_int(ofp, pidx) != 4) ||
+       (fwrite(T, sizeof(sauchar_t), m, ofp) != m)) {
+      fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
       perror(NULL);
       exit(EXIT_FAILURE);
     }
   }
-  if(ferror(stdin)) {
-    fprintf(stderr, "%s: Cannot read from `stdin': ", argv[0]);
+  if(ferror(fp)) {
+    fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
     perror(NULL);
     exit(EXIT_FAILURE);
   }
   finish = clock();
-  fprintf(stderr, "%d bytes: %.4f sec\n",
-    (int)n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
+  fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n",
+    n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
+
+  /* Close files */
+  if(needclose & 1) { fclose(fp); }
+  if(needclose & 2) { fclose(ofp); }
 
   /* Deallocate memory. */
-  free(T);
   free(SA);
+  free(T);
 
   return 0;
 }