diff options
| -rw-r--r-- | kmer_utils.c | 11 |
1 files changed, 8 insertions, 3 deletions
diff --git a/kmer_utils.c b/kmer_utils.c index 5d3b8a5..a154cb2 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -222,6 +222,9 @@ void count_sequence(const char *seq, const size_t seq_length, const unsigned int unsigned long long multiply = 1; // for each char in the k-mer check if it is an error char + + // TODO Get rid of branch prediction - can we do it? Error flag with + // bitshifts for(i = position + kmer - 1; i >= position; i--){ if(seq[i] == 5) { position = i; @@ -272,18 +275,19 @@ array_type * get_kmer_counts_from_file(array_type *counts, FILE *fh, const unsig exit(EXIT_FAILURE); } + // TODO remove getdelim and add a fasta parsing state engine instead while ((read = getdelim(&line, &len, '>', fh)) != -1) { size_t k; char *seq; - // find our first \n, this should be the end of the header + // TODO optimize out strchr with a while loop seq = strchr(line, '\n'); if(seq == NULL) continue; - // point to one past that. seq = seq + 1; + // TODO can we loop jam the strnstrip and alpha? that way memory access is only done once? // strip out all other newlines to handle multiline sequences const size_t seq_length = strnstrip(seq, '\n', strlen(seq)); @@ -295,6 +299,7 @@ array_type * get_kmer_counts_from_file(array_type *counts, FILE *fh, const unsig count_sequence(seq, seq_length, kmer, counts); if(count_compliment) { + // TODO Same for this, can we reverse and compliment at the same time? for(k = 0; k < seq_length; k++) { seq[k] = compliment[(int)seq[k]]; } @@ -305,7 +310,7 @@ array_type * get_kmer_counts_from_file(array_type *counts, FILE *fh, const unsig } } - free(line); + free(line); fclose(fh); return counts; |