diff options
Diffstat (limited to 'src/c/multifasta_to_otu.c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 32 |
1 files changed, 3 insertions, 29 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 9a9ee88..1ae1802 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -21,10 +21,6 @@ #define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --input-filelist\n\ta file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing 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-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version." -static int cmp (const void * a, const void * b) { - return ( *(double*)a - *(double*)b ); -} - char **get_fasta_files_from_file(char *fn) { char **files; int files_count = 0; @@ -336,7 +332,7 @@ int main(int argc, char **argv) { printf("Beginning to process samples\n"); - #pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences) + #pragma omp parallel for shared(solutions, sensing_matrix_ptr, done) for(size_t i = 0; i < dir_count; i++ ) { size_t x = 0; @@ -356,8 +352,6 @@ int main(int argc, char **argv) { // load counts matrix double *count_matrix = malloc(width * sizeof(double)); check_malloc(count_matrix, NULL); - double *sorted_count_matrix = malloc(width * sizeof(double)); - check_malloc(sorted_count_matrix, NULL); // convert our matrix into doubles { @@ -365,33 +359,13 @@ int main(int argc, char **argv) { for(x = 0; x < width; x++) { count_matrix[x] = (double)integer_counts[x]; - sorted_count_matrix[x] = count_matrix[x]; } free(integer_counts); } - // sort our array - qsort(sorted_count_matrix, width, sizeof(double), cmp); - - // get our "rare" counts - for(y = 0; y < width; y++) { - double percentage = 0; - - rare_value = sorted_count_matrix[y]; - rare_width = 0; - for(x = 0; x < width; x++) { - if(count_matrix[x] <= rare_value) { - rare_width++; - } - } - percentage = (double)rare_width / (double)width; - - if(percentage >= rare_percent) - break; - } - - free(sorted_count_matrix); + // get_rare_value + get_rare_value(count_matrix, width, rare_percent, &rare_value, &rare_width); if(verbose) printf("there are %llu values less than %llu\n", rare_width, rare_value); |