diff options
| author | Calvin Morrison <mutantturkey@gmail.com> | 2013-09-14 12:58:13 -0400 |
|---|---|---|
| committer | Calvin Morrison <mutantturkey@gmail.com> | 2013-09-14 12:58:13 -0400 |
| commit | 8d1e990611a128d123e47f8a068ff9b045794db4 (patch) | |
| tree | 3a7154e0bee1809c0e29fd7df646e64491b3c28a | |
| parent | 4ae5cfe9e627429ee4d27390da9eb07a410f8831 (diff) | |
improve performance of convert_kmer_to_index by using a bitwise OR to convert our characters to lowercare: str[i] | Ox20, and reduce the number of switches as a result
| -rw-r--r-- | kmer_total_count.c | 3 | ||||
| -rw-r--r-- | kmer_utils.c | 14 |
2 files changed, 7 insertions, 10 deletions
diff --git a/kmer_total_count.c b/kmer_total_count.c index 23ca512..6d07e13 100644 --- a/kmer_total_count.c +++ b/kmer_total_count.c @@ -13,8 +13,9 @@ int main(int argc, char **argv) { char *line = NULL; size_t len = 0; ssize_t read; + long i = 0; + unsigned int kmer = 0; - unsigned long i = 0; unsigned long width = 0; unsigned long long *counts; diff --git a/kmer_utils.c b/kmer_utils.c index e737346..c0441e2 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -16,27 +16,23 @@ // long kmer - how long of a index value you want to return // long error_pos - what index to return for a non ACGT character // -inline long convert_kmer_to_index(const char *str, long kmer, long error_pos) { +inline long convert_kmer_to_index(const char *str, int kmer, long error_pos) { - long i = 0; - long out = 0; - long multiply = 1; + int i = 0; + unsigned long out = 0; + unsigned long multiply = 1; for(i = kmer - 1; i >= 0; i--){ - switch(str[i]) { + switch(str[i] | 0x20 ) { case 'a': - case 'A': break; case 'c': - case 'C': out += 1 * multiply; break; case 'g': - case 'G': out += 2 * multiply; break; case 't': - case 'T': out += 3 * multiply; break; default: |