From 592e0945fcfb94d641c16f2cf02add0c0430b226 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Tue, 4 Mar 2014 14:19:46 -0500
Subject: fix all warnings and that weird bug
---
src/c/kmer_utils.c | 4 ++--
src/c/multifasta_to_otu.c | 10 +++++-----
src/c/quikr.c | 2 +-
src/c/quikr_functions.c | 1 -
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();
--
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