From 2c038ba630c14c7030186c64e9eb92761ddcba74 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 6 Mar 2014 17:05:40 -0500 Subject: 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 --- kmer_utils.h | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'kmer_utils.h') 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); -- cgit v1.2.3