kmer utils too

1 files changed, 35 insertions, 10 deletions

diff --git a/kmer_utils.h b/kmer_utils.h
index a727da8..9fcc03c 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,5 +1,9 @@
 // dna-util's function library.
+#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);
 char *index_to_kmer(unsigned long long index, long kmer);
 
@@ -15,31 +19,52 @@ void reverse_string(char *s, size_t len);
 // quicky calculate 4^x 
 unsigned long long pow_four(unsigned long long x);
 
-// check if pointer is null. a helper for dealing with NULL
+// check if pointer is null. a helper for dealing with NULL 
 // return values as errors. Calls strerror and quits if 
 // ptr is null, optionally takes *error char array as 
 // a error to output
 void check_null_ptr(void *ptr, const char *error);
 
-void count_sequence(const char *seq, const size_t seq_length, const unsigned int kmer, unsigned long long *counts);
+template <typename array_type>
+void count_sequence(const char *seq, const size_t seq_length, const unsigned int kmer, array_type *counts);
 
 // Variables
-//
-const unsigned char alpha[256]; 
-const unsigned char reverse_alpha[4];
-const unsigned char compliment[5];
+typedef struct {
+	size_t operator() (const size_t &k) const {
+	return k;
+	}
+} kmer_noHash_hash;
 
+typedef struct {
+	bool operator() (const size_t &x, const size_t &y) const {
+		return x == y;
+	}
+} kmer_eq; 
 
-// file loading functions
+typedef unordered_map<size_t,unsigned long long, kmer_noHash_hash, kmer_eq> kmer_map;
+
+unsigned char alpha[256]; 
+unsigned char reverse_alpha[4];
+unsigned char compliment[5];
 
 // open file from filename in char array *fn, and try and parse in one mer per
 // line, of size kmer, and store the indicies of those mers in the *arr
 // pointer;
 unsigned long long load_specific_mers_from_file(const char *fn, unsigned int kmer, size_t width, size_t *arr);
 
-unsigned long long * get_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment);
-unsigned long long * get_kmer_counts_from_file(FILE *fh, const int kmer, const bool count_compliment);
-
 unsigned long long * get_continuous_kmer_counts_from_filename(const char *fn, const unsigned int kmer, const bool count_compliment);
 unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer, const bool count_compliment);
 
+
+template <typename array_type>
+array_type * get_kmer_counts_from_file(array_type *counts, FILE *fh, const unsigned int kmer, const bool count_compliment);
+
+kmer_map           *get_kmer_counts_from_filename(kmer_map           *counts, const char *fn, const unsigned int kmer, const bool count_compliment);
+unsigned long long *get_kmer_counts_from_filename(unsigned long long *counts, const char *fn, const unsigned int kmer, const bool count_compliment);
+
+
+size_t load_specific_mers_from_file(char *fn, unsigned int kmer, size_t width, size_t *arr);
+
+// print functions
+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);