diff options
Diffstat (limited to 'src/c')
| -rw-r--r-- | src/c/kmer_utils.c | 4 | ||||
| -rw-r--r-- | src/c/multifasta_to_otu.c | 10 | ||||
| -rw-r--r-- | src/c/quikr.c | 2 | ||||
| -rw-r--r-- | src/c/quikr_functions.c | 1 | ||||
| -rw-r--r-- | src/c/test.c | 4 |
5 files changed, 9 insertions, 12 deletions
diff --git a/src/c/kmer_utils.c b/src/c/kmer_utils.c index ca33156..0980a69 100644 --- a/src/c/kmer_utils.c +++ b/src/c/kmer_utils.c @@ -28,7 +28,7 @@ unsigned long num_to_index(const char *str, const int kmer, const long error_pos for(i = kmer - 1; i >= 0; i--){ - if(str[i] >> 2) { + if(str[i] == 5) { // position += i; return error_pos; } @@ -117,7 +117,7 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in // strip out all other newlines to handle multiline sequences str = strnstrip(start, str, '\n',start_len); - size_t seq_length = strlen(str); + ssize_t seq_length = strlen(str); if(seq_length < kmer) continue; diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 7513b11..fcb0822 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -38,7 +38,7 @@ char **get_fasta_files(char *directory) { exit(EXIT_FAILURE); } - while(e = readdir(dh)) + while((e = readdir(dh))) count++; e = NULL; @@ -226,11 +226,11 @@ int main(int argc, char **argv) { struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer); double *sensing_matrix_ptr = sensing_matrix->matrix; - unsigned long long sequences = sensing_matrix->matrix; + unsigned long long sequences = sensing_matrix->sequences; if(verbose) { printf("directory count: %llu\n", dir_count); - printf("width: %llu\nsequences %llu\n", width, sensing_matrix->sequences); + printf("width: %llu\nsequences %llu\n", width, sequences); } unsigned long long *solutions = malloc(dir_count * sequences * sizeof(unsigned long long)); @@ -244,7 +244,7 @@ int main(int argc, char **argv) { #endif printf("Beginning to process samples\n"); #pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences) - for(long i = 0; i < dir_count; i++ ) { + for(size_t i = 0; i < dir_count; i++ ) { unsigned long long x = 0; unsigned long long y = 0; @@ -343,7 +343,7 @@ int main(int argc, char **argv) { double *solution = nnls(sensing_matrix_rare, count_matrix_rare, sequences, rare_width); // add the current solution to the solutions array - for(int z = 0; z < sequences; z++ ) { + for(unsigned long long z = 0; z < sequences; z++ ) { solutions[sensing_matrix->sequences*i + z] = (unsigned long long)round(solution[z] * file_sequence_count); } diff --git a/src/c/quikr.c b/src/c/quikr.c index bbe6a31..180a548 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -116,7 +116,7 @@ int main(int argc, char **argv) { } if(verbose) { - printf("rare width:%ld\n", rare_width); + printf("rare width:%llu\n", rare_width); printf("kmer: %u\n", kmer); printf("lambda: %llu\n", lambda); printf("fasta: %s\n", input_fasta_filename); diff --git a/src/c/quikr_functions.c b/src/c/quikr_functions.c index 178c1d1..89f0698 100644 --- a/src/c/quikr_functions.c +++ b/src/c/quikr_functions.c @@ -21,7 +21,6 @@ void check_malloc(void *ptr, char *error) { } } - void debug_arrays(double *count_matrix, struct matrix *sensing_matrix) { FILE *count_fh = fopen("count.mat", "w"); FILE *sensing_fh = fopen("sensing.mat", "w"); diff --git a/src/c/test.c b/src/c/test.c index fa905af..0122dc3 100644 --- a/src/c/test.c +++ b/src/c/test.c @@ -60,7 +60,6 @@ void test_normalize_matrix() { int test_number = 1; int fail_flag = 0; char *test_name = "test_normailze_matrix"; - char *type = "%lf"; double sum = 0; int i = 0; @@ -106,8 +105,7 @@ void test_normalize_matrix() { } -int main(int argc, char **argv) { - int test_number = 1; +int main() { header("count_sequences"); test_count_sequences(); |