diff options
| -rw-r--r-- | kmer_utils.h | 20 |
1 files changed, 17 insertions, 3 deletions
diff --git a/kmer_utils.h b/kmer_utils.h index 9fcc03c..f5087f2 100644 --- a/kmer_utils.h +++ b/kmer_utils.h @@ -43,9 +43,23 @@ typedef struct { 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]; +const unsigned char alpha[256] = +{5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 0, 5, 1, 5, 5, 5, 2, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, +5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5}; +const char reverse_alpha[4] = { 'A', 'C', 'G', 'T' }; + + // compliments + // A C G T E E + // T G C A E E +const char compliment[6] = { 3, 2, 1, 0, 5, 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 |