add kmercounting code from dna-utils. update our make file to support debugging, and update quikr to count-kmer code internally

1 files changed, 11 insertions, 0 deletions

diff --git a/src/c/kmer_utils.h b/src/c/kmer_utils.h
new file mode 100644
index 0000000..34cedca
--- /dev/null
+++ b/src/c/kmer_utils.h
@@ -0,0 +1,11 @@
+// Kmer functions
+void convert_kmer_to_num(char *str, const unsigned long length);
+unsigned long long * get_kmer_counts_from_file(const char *fn, const int kmer);
+unsigned long num_to_index(const char *str, const int kmer, int *position, const long error_pos);
+
+// Utility functions
+char *strnstrip(const char *s, char *dest, int c, int len);
+unsigned long long pow_four(unsigned long long x);
+
+// Variables
+const unsigned char alpha[256];