reverse compliment

1 files changed, 29 insertions, 6 deletions

diff --git a/kmer_utils.h b/kmer_utils.h
index 4bc732a..a727da8 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -1,22 +1,45 @@
-// Kmer functions
-void convert_kmer_to_num(char *str, const unsigned long length);
+// dna-util's function library.
+
 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);
 
 // Utility functions
+
+
+// strip char 'c' out of char array *s of length len
 size_t strnstrip(char *s, int c, size_t len);
+
+// reverse char arry *s of length len
+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
+// 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);
+
 // Variables
+//
 const unsigned char alpha[256]; 
+const unsigned char reverse_alpha[4];
+const unsigned char compliment[5];
+
 
 // file loading functions
+
+// 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);
-unsigned long long * get_kmer_counts_from_file(FILE *fh, const int kmer);
+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);
-unsigned long long * get_continuous_kmer_counts_from_file(FILE *fh, const unsigned int kmer);
+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);