add kmer_continuous_count

this tool will count continuously, instead of line by line. The way that
this works out is something like this:

test.fa
> header 1
AAAAATTTTT
> header 2
GGGGGAAAAA

counting 6 mers, the program will count TTTGGG,  TTGGGG, TGGGGG, like
there was no header seperating them. This can be useful for certain
tyeps of processing, like when the sequences are continuous from a
genome.

initial commit

1 files changed, 4 insertions, 0 deletions

diff --git a/kmer_utils.h b/kmer_utils.h
index ceb28eb..ae48136 100644
--- a/kmer_utils.h
+++ b/kmer_utils.h
@@ -12,5 +12,9 @@ const unsigned char alpha[256];
 
 // file loading functions
 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_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);