diff options
Diffstat (limited to 'kmer_locations.c')
| -rw-r--r-- | kmer_locations.c | 55 |
1 files changed, 40 insertions, 15 deletions
diff --git a/kmer_locations.c b/kmer_locations.c index fbfcab4..56bf934 100644 --- a/kmer_locations.c +++ b/kmer_locations.c @@ -8,14 +8,24 @@ #include "kmer_utils.h" -void print_mer(unsigned long long mer, long long pos, bool labels, bool reverse, unsigned int kmer) { +void print_mer(unsigned long long mer, long const long pos, const bool labels, const bool reverse, unsigned int kmer, char *label) { if(labels) { - char *kmer_str = index_to_kmer(mer, kmer); + char *kmer_str; + bool free_ptr = false; + if(label == NULL) { + kmer_str = index_to_kmer(mer, kmer); + free_ptr = true; + } + else { + kmer_str = label; + } + if(reverse) printf("%s %llu c\n", kmer_str, pos); else printf("%s %llu\n", kmer_str, pos); - free(kmer_str); + if (free_ptr) + free(kmer_str); } else { if(reverse) @@ -30,6 +40,7 @@ void print_sequence(const char *seq, // sequence const size_t global_pos, // overall position in read const unsigned int kmer, // kmer size size_t *specific_mers, // specific mers array + char **specific_mers_labels, // specific mers array size_t num_specific_mers, bool labels, // print label instead of indicies bool reverse) // reverse points @@ -60,11 +71,11 @@ void print_sequence(const char *seq, // sequence size_t j; for(j = 0; j < num_specific_mers; j++) { if(mer == specific_mers[j]) - print_mer(mer, position + global_pos, labels, reverse, kmer); + print_mer(mer, position + global_pos, labels, reverse, kmer, specific_mers_labels[j]); } } else { - print_mer(mer, position + global_pos, labels, reverse, kmer); + print_mer(mer, position + global_pos, labels, reverse, kmer, NULL); } // skip count if error next: ; @@ -110,14 +121,13 @@ int main(int argc, char **argv) { char *mer_fn = NULL; size_t num_desired_indicies = 0; size_t *desired_indicies = NULL; + char **labeled_mers = NULL; bool label = false; bool kmer_set = false; bool specific_mers = false; bool count_compliment = false; - unsigned long long width = 0; - static struct option long_options[] = { {"input", required_argument, 0, 'i'}, {"kmer", required_argument, 0, 'k'}, @@ -150,7 +160,7 @@ int main(int argc, char **argv) { count_compliment = true; break; case 'm': - specific_mers = false; + specific_mers = true; mer_fn = optarg; break; case 'l': @@ -193,14 +203,23 @@ int main(int argc, char **argv) { } if(specific_mers) { + size_t j; + size_t width = pow_four(kmer); desired_indicies = (size_t *) malloc((width) * sizeof(size_t)); if(desired_indicies == NULL) exit(EXIT_FAILURE); + num_desired_indicies = load_specific_mers_from_file(mer_fn, kmer, width, desired_indicies); if(num_desired_indicies == 0) { fprintf(stderr, "Error: no mers loaded from file\n"); exit(EXIT_FAILURE); } + + labeled_mers = (char**) malloc(sizeof(char **)); + check_null_ptr(labeled_mers, NULL); + for(j = 0; j < num_desired_indicies; j++) { + labeled_mers[j] = index_to_kmer(desired_indicies[j], kmer); + } } @@ -226,23 +245,29 @@ int main(int argc, char **argv) { seq[k] = alpha[(int)seq[k]]; } - print_sequence(seq, seq_length, global_position, kmer, desired_indicies, num_desired_indicies, label, false); + print_sequence(seq, seq_length, global_position, kmer, desired_indicies, labeled_mers, num_desired_indicies, label, false); if(count_compliment) { for(k = 0; k < seq_length; k++) { seq[k] = compliment[(int)seq[k]]; } - reverse_string(seq, seq_length); - print_sequence(seq, seq_length, global_position, kmer, desired_indicies, num_desired_indicies, label, true); - } + size_t rev_seq_length = seq_length; + + // chomp all errors off the beginning + while(*seq == 5) { + rev_seq_length--; + seq++; + } - if(seq[seq_length - 1] == '>') - seq_length --; + print_sequence(seq, rev_seq_length, global_position, kmer, desired_indicies, labeled_mers, num_desired_indicies, label, true); + } + if(seq_length != 0) { + seq_length--; + } sequence++; global_position += seq_length; - printf("%llu %llu\n", seq_length, global_position); } free(line); |