diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2013-10-28 12:08:58 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2013-10-28 12:08:58 -0400 |
| commit | a6a9c32bae2aa0b620c7ea4497885f23bdf84265 (patch) | |
| tree | 88e4583cfffdb5eea5cc76492ca0610cd533eb22 | |
| parent | 3f20f3ba6b9b7375290ea8342dcca4e3e977829e (diff) | |
update kmer utils
| -rw-r--r-- | src/c/kmer_utils.c | 10 |
1 files changed, 4 insertions, 6 deletions
diff --git a/src/c/kmer_utils.c b/src/c/kmer_utils.c index cf8d666..3a1eba4 100644 --- a/src/c/kmer_utils.c +++ b/src/c/kmer_utils.c @@ -4,6 +4,8 @@ #include <stdlib.h> #include <string.h> +#include "quikr.h" + 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, @@ -16,13 +18,9 @@ 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}; -inline unsigned long long pow_four(unsigned long long x) { - return (unsigned long long)1 << (x * 2); -} - // convert a string of k-mer size base-4 values into a // base-10 index -inline unsigned long num_to_index(const char *str, const int kmer, int *position, const long error_pos) { +unsigned long num_to_index(const char *str, const int kmer, const long error_pos) { int i = 0; unsigned long out = 0; @@ -31,7 +29,7 @@ inline unsigned long num_to_index(const char *str, const int kmer, int *position for(i = kmer - 1; i >= 0; i--){ if(str[i] >> 2) { - position += i; + // position += i; return error_pos; } |