diff options
Diffstat (limited to 'kmer_utils.h')
| -rw-r--r-- | kmer_utils.h | 14 |
1 files changed, 10 insertions, 4 deletions
diff --git a/kmer_utils.h b/kmer_utils.h index af13227..cf7b8a1 100644 --- a/kmer_utils.h +++ b/kmer_utils.h @@ -1,3 +1,6 @@ +#include <unordered_map> +using namespace std; + // Kmer functions void convert_kmer_to_num(char *str, const unsigned long length); unsigned long num_to_index(const char *str, const int kmer, const long error_pos, long long *current_position); @@ -8,13 +11,16 @@ size_t strnstrip(char *s, int c, size_t len); unsigned long long pow_four(unsigned long long x); // Variables -const unsigned char alpha[256]; +typedef unordered_map<size_t,unsigned long long> kmer_map; // file loading functions -node * get_sparse_kmer_counts_from_filename(const char *fn, const unsigned int kmer); -node * get_sparse_kmer_counts_from_file(FILE *fh, const int kmer); +kmer_map *get_sparse_kmer_counts_from_filename(const char *fn, const unsigned int kmer); +kmer_map *get_sparse_kmer_counts_from_file(FILE *fh, int kmer); unsigned long long * get_dense_kmer_counts_from_file(FILE *fh, const unsigned int kmer); -void print_dense(unsigned long long *counts, bool label, bool nonzero, unsigned int kmer); +void print_kmer(unsigned long long *counts, bool label, bool nonzero, unsigned int kmer); +void print_kmer(kmer_map *counts, bool label, bool nonzero, unsigned int kmer); + +unsigned char alpha[256]; |