use longs instead of ints, fix a mistake in the --help

3 files changed, 20 insertions, 19 deletions

diff --git a/CHANGELOG b/CHANGELOG
index d8d3b79..002b265 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -8,9 +8,10 @@ May 16th 2013, 1.0.1 Released
 May 20th 2013, 1.0.2 Released
 - correted usage strings
 - install manpages globally (to {PREFIX}/share/man/man1)
-- added native gzip decoding for quikr and multifasta_to_otu
 
 Current Development Branch
 - Licensing files and documentation added
 - Removed unused code from the NBC project
 - Fixed a overflow bug in quikr_train
+- added native gzip decoding for quikr and multifasta_to_otu
+- documentation fixes
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index 2f4bf87..e0fb128 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -26,14 +26,14 @@ int main(int argc, char **argv) {
 
   double *sensing_matrix;
 
-  long int width = 0;
-  long int sequences = 0;
+  long width = 0;
+  long sequences = 0;
 
   int kmer = 6;
   int lambda = 10000;
 
-  int x = 0;
-  int y = 0;
+  long x = 0;
+  long y = 0;
 
   int jobs = 1;
   #ifdef Linux
@@ -150,7 +150,7 @@ int main(int argc, char **argv) {
   } 
 
   // do a directory count
-  int dir_count = -2; // -2 for ../ and ./
+  long dir_count = -2; // -2 for ../ and ./
   while(entry = readdir(input_directory_dh)) 
     dir_count++; 
   rewinddir(input_directory_dh);
@@ -167,7 +167,7 @@ int main(int argc, char **argv) {
   }
 
   if(verbose) {
-    printf("directory count: %d\n", dir_count);
+    printf("directory count: %ld\n", dir_count);
     printf("width: %ld\nsequences %ld\n", width, sequences);
   }
 
@@ -197,7 +197,7 @@ int main(int argc, char **argv) {
     exit(EXIT_FAILURE);
   }
 
-  int *file_sequence_count = malloc(dir_count * sizeof(int));
+  long *file_sequence_count = malloc(dir_count * sizeof(long));
   if(file_sequence_count == NULL) {
     fprintf(stderr, "Could not allocate enough memory\n");
     exit(EXIT_FAILURE);
@@ -206,12 +206,12 @@ int main(int argc, char **argv) {
   struct dirent result;
 
   omp_set_num_threads(jobs);
-  int done = 0;
+  long done = 0;
   printf("Beginning to process samples\n"); 
 #pragma omp parallel for shared(solutions, sequences, width, result, done)
-  for(int i = 0; i < dir_count; i++ ) {
+  for(long i = 0; i < dir_count; i++ ) {
 
-    int z = 0;
+    long z = 0;
     struct dirent *directory_entry;
     char *filename = malloc(256 * sizeof(char));
     char *base_filename = malloc(256 * sizeof(char));
@@ -269,7 +269,7 @@ int main(int argc, char **argv) {
     }
 
     done++;
-    printf("%d/%d samples processed\n", done, dir_count); 
+    printf("%ld/%ld samples processed\n", done, dir_count); 
     free(solution);
     free(count_matrix);
     free(filename);
diff --git a/src/c/quikr.c b/src/c/quikr.c
index 17d6480..f588c5f 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -12,7 +12,7 @@
 #include "quikr_functions.h"
 
 #define sensing_matrix(i,j) (sensing_matrix[width*i + j])
-#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, read manpage for more details"
+#define USAGE "Usage:\n\tquikr [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, read manpage for more details"
 
 int main(int argc, char **argv) {
 
@@ -24,8 +24,8 @@ int main(int argc, char **argv) {
   char *sensing_fasta_filename = NULL;
   char *output_filename = NULL;
 
-  int x = 0;
-  int y = 0;
+  long x = 0;
+  long y = 0;
 
   int verbose = 0;
   int debug = 0;
@@ -33,8 +33,8 @@ int main(int argc, char **argv) {
   int lambda = 10000;
   int kmer = 6;
 
-  int width = 0;
-  int sequences = 0;
+  long width = 0;
+  long sequences = 0;
 
   while (1) {
     static struct option long_options[] = {
@@ -144,7 +144,7 @@ int main(int argc, char **argv) {
   }
 
   if(verbose) {
-    printf("width: %d\nsequences %d\n", width, sequences);
+    printf("width: %ld\nsequences %ld\n", width, sequences);
   }
 
   double *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, sequences, width);
@@ -157,7 +157,7 @@ int main(int argc, char **argv) {
     }
   }
 
-  for(x= 0; x < sequences; x++) {
+  for(x = 0; x < sequences; x++) {
     sensing_matrix(x, 0) = 1.0;
   }
   // normalize our count_matrix