diff options
Diffstat (limited to 'src/c')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 45 |
1 files changed, 24 insertions, 21 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 9266e21..aa9f821 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -36,11 +36,11 @@ char **get_fasta_files_from_file(char *fn) { size_t len = 0; char *line = NULL; - FILE *fh = fopen(fn, "r"); - if(fh == NULL) { - fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno)); - exit(EXIT_FAILURE); - } + FILE *fh = fopen(fn, "r"); + if(fh == NULL) { + fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno)); + exit(EXIT_FAILURE); + } files = malloc(sizeof(char **)); @@ -62,9 +62,9 @@ char **get_fasta_files_from_file(char *fn) { fprintf(stderr, "could not realloc keys\n"); exit(EXIT_FAILURE); } - } + } else { - fprintf(stderr, "Warning: ignoring %s (%s)\n", file, strerror(errno)); + fprintf(stderr, "Warning: ignoring %s (%s)\n", file, strerror(errno)); errno = 0; free(file); } @@ -98,7 +98,7 @@ char **get_fasta_files_from_directory(char *directory) { exit(EXIT_FAILURE); } - while((e = readdir(dh))) + while((e = readdir(dh))) count++; e = NULL; @@ -125,14 +125,14 @@ char **get_fasta_files_from_directory(char *directory) { ext = strrchr(e->d_name, '.'); - if(str_eq(ext, ".fasta") || + if(str_eq(ext, ".fasta") || str_eq(ext, ".fa") || str_eq(ext, ".fna")) { char *header = malloc(strlen(directory) + strlen(e->d_name) + 1); check_malloc(header, NULL); - sprintf(header, "%s/%s", directory, e->d_name); + sprintf(header, "%s/%s", directory, e->d_name); headers[array_pos] = header; } else { @@ -277,14 +277,14 @@ int main(int argc, char **argv) { exit(EXIT_FAILURE); } - if(verbose) { + if(verbose) { printf("kmer: %u\n", kmer); printf("lambda: %llu\n", lambda); printf("input directory: %s\n", input_fasta_directory); printf("input filelist: %s\n", input_fasta_filelist); printf("sensing database: %s\n", sensing_matrix_filename); printf("output: %s\n", output_filename); - printf("number of jobs to run at once: %d\n", jobs); + printf("number of jobs to run at once: %d\n", jobs); } if(access (sensing_matrix_filename, F_OK) == -1) { @@ -336,9 +336,9 @@ int main(int argc, char **argv) { #endif - printf("Beginning to process samples\n"); + 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, width, done, sequences) for(size_t i = 0; i < dir_count; i++ ) { size_t x = 0; @@ -347,7 +347,7 @@ int main(int argc, char **argv) { unsigned long long file_sequence_count = 0; unsigned long long rare_value = 0; - unsigned long long rare_width = 0; + unsigned long long rare_width = 0; double rare_percent = 1.0; @@ -396,7 +396,7 @@ int main(int argc, char **argv) { if(verbose) printf("there are %llu values less than %llu\n", rare_width, rare_value); - // add a extra space for our zero's array + // add a extra space for our zero's array, so we can set the first column to 1's rare_width++; // store our count matrix @@ -408,11 +408,13 @@ int main(int argc, char **argv) { // copy only kmers from our original counts that match our rareness percentage // in both our count matrix and our sensing matrix - for(x = 0, y = 1; x < width; x++) { + // + // y = 1 because we are offsetting the array by 1, so we can set the first row to all 1's + for(x = 0, y = 1; x < width - 1; x++) { if(count_matrix[x] <= rare_value) { count_matrix_rare[y] = count_matrix[x]; - for(z = 0; z < sequences; z++) + for(z = 0; z < sequences; z++) sensing_matrix_rare[z*rare_width + y] = sensing_matrix_ptr[z*width + x]; y++; @@ -424,9 +426,10 @@ int main(int argc, char **argv) { normalize_matrix(sensing_matrix_rare, sequences, rare_width); // multiply our kmer counts and sensing matrix by lambda - for(x = 1; x < rare_width; x++) + for(x = 1; x < rare_width; x++) count_matrix_rare[x] *= lambda; + //TODO use one loop for(x = 0; x < sequences; x++) { for(y = 1; y < rare_width; y++) { sensing_matrix_rare[rare_width*x + y] *= lambda; @@ -455,7 +458,7 @@ int main(int argc, char **argv) { } done++; - printf("%ld/%llu samples processed\n", done, dir_count); + printf("%ld/%llu samples processed\n", done, dir_count); free(solution); free(count_matrix_rare); free(count_matrix); @@ -464,7 +467,7 @@ int main(int argc, char **argv) { // output our matrix FILE *output_fh = fopen(output_filename, "w"); - if(output_fh == NULL) { + if(output_fh == NULL) { fprintf(stderr, "Could not open %s for writing\n", output_filename); exit(EXIT_FAILURE); } |