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Diffstat (limited to 'kmer_utils.c')
-rw-r--r--kmer_utils.c64
1 files changed, 55 insertions, 9 deletions
diff --git a/kmer_utils.c b/kmer_utils.c
index 2b3ce67..b0cab47 100644
--- a/kmer_utils.c
+++ b/kmer_utils.c
@@ -26,7 +26,7 @@ inline unsigned long long pow_four(unsigned long long x) {
// convert a string of k-mer size base-4 values into a
// base-10 index
-inline unsigned long num_to_index(const char *str, const int kmer, const long error_pos) {
+inline unsigned long num_to_index(const char *str, const int kmer, const long error_pos, size_t *current_position) {
int i = 0;
unsigned long out = 0;
@@ -35,9 +35,7 @@ inline unsigned long num_to_index(const char *str, const int kmer, const long er
for(i = kmer - 1; i >= 0; i--){
if(str[i] == 5) {
- #ifndef SHARED
- position += i;
- #endif
+ current_position += i;
return error_pos;
}
@@ -48,11 +46,59 @@ inline unsigned long num_to_index(const char *str, const int kmer, const long er
return out;
}
+// return the number of loaded elements
+unsigned long long load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr) {
+ FILE *fh;
+ size_t arr_pos = 0;
+ char line[64];
+
+ fh = fopen(fn, "r");
+ if(fh == NULL) {
+ fprintf(stderr, "Error opening %s - %s\n", fn, strerror(errno));
+ exit(EXIT_FAILURE);
+ }
+
+ while (fgets(line, sizeof(line), fh) != NULL) {
+ size_t i;
+ size_t len;
+
+ len = strlen(line);
+ if(len == 0)
+ continue;
+
+ len--;
+ line[len] = '\0';
+
+
+ if(len != kmer) {
+ fprintf(stderr, "SKIPPING: '%s' is not length %u\n", line, kmer);
+ continue;
+ }
+
+ for(i = 0; i < len; i++) {
+ line[i] = alpha[(int)line[i]];
+ }
+
+ size_t mer = num_to_index(line, kmer, width, NULL);
+ if(mer == width) {
+ fprintf(stderr, "SKIPPING: '%s' is a unrecognized mer\n", line);
+ continue;
+ }
+ else {
+ arr[arr_pos] = mer;
+ arr_pos++;
+ }
+ }
+
+ fclose(fh);
+ return arr_pos;
+}
+
// convert an index back into a kmer string
char *index_to_kmer(unsigned long long index, long kmer) {
- int i = 0;
- int j = 0;
+ size_t i = 0;
+ size_t j = 0;
char *num_array = calloc(kmer, sizeof(char));
char *ret = calloc(kmer + 1, sizeof(char));
if(ret == NULL)
@@ -74,7 +120,7 @@ char *index_to_kmer(unsigned long long index, long kmer) {
// our offset for how many chars we prepended
int offset = j;
// save i so we can print it
- int start = i ;
+ size_t start = i ;
// decrement i by 1 to reverse the last i++
i--;
@@ -116,8 +162,8 @@ unsigned long long * get_kmer_counts_from_file(const char *fn, const unsigned in
size_t len = 0;
ssize_t read;
- long long i = 0;
- long long position = 0;
+ size_t i = 0;
+ size_t position = 0;
FILE * const fh = fopen(fn, "r");
if(fh == NULL) {