diff options
Diffstat (limited to 'kmer_utils.c')
| -rw-r--r-- | kmer_utils.c | 64 |
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) { |