diff --git a/src/kr_aligner.c b/src/kr_aligner.c
index 82746d53ed0c496d9836e3f61e86ba9f2c0ee6ef..44981f265b1bbf9ca08b2ae47db4c0fc832f4bc9 100644
--- a/src/kr_aligner.c
+++ b/src/kr_aligner.c
@@ -15,6 +15,19 @@ typedef struct {
seq_t * seq;
} hashed_object_t;
+/* Compare must return the distance between the object and the value.
+ * So 0 correspond to match
+ */
+int compare (const void* arg, const void* obj) {
+ hashed_object_t * hashed = (hashed_object_t *)obj;
+ uint64_t hash = *((uint64_t *)arg);
+
+ if (hash == hashed->kmers[0].hash || hash == hashed->kmers[1].hash)
+ return 0;
+ else
+ return 1;
+}
+
/* Hashtable to store all the reads and main kmers regarding the hashed value of the kmer */
static tommy_hashdyn hashtable;
@@ -33,8 +46,13 @@ int kr_init (uint nb_seqs, kmer_t * kmers, seq_t * sequences) {
object->kmers = kmers + idx*2;
object->seq = sequences + idx;
- tommy_hashdyn_insert(&hashtable, &object->node, object, object->kmers[0].hash);
- tommy_hashdyn_insert(&hashtable, &object->node, object, object->kmers[1].hash);
+ tommy_hashdyn_insert(&hashtable, &(object->node), object, object->kmers[0].hash);
+
+ object = malloc(sizeof(hashed_object_t));
+ object->kmers = kmers + idx*2;
+ object->seq = sequences + idx;
+
+ tommy_hashdyn_insert(&hashtable, &(object->node), object, object->kmers[1].hash);
}
return TRUE;
@@ -57,29 +75,23 @@ typedef struct {
void search_hash (uint64_t h, seq_t * ref, uint seq_offset, result_t * result) {
/* search for the hash value */
- tommy_node* i = tommy_hashdyn_bucket(&hashtable, h);
- uint nb_obj = 0;
+ hashed_object_t * obj = tommy_hashdyn_search(&hashtable, compare, &h, h);
+
+ // Init
+ result->seq = NULL;
- /* Look for possible collided values */
- while (i) {
- hashed_object_t * obj = i->data;
+ if (obj) {
if (h == obj->kmers[0].hash && verify_sequence(ref, seq_offset, obj)) {
/* Create the result */
result->offset = seq_offset-obj->kmers[0].offset;
result->seq = obj->seq;
result->direction = '+';
- break;
} else if (h == obj->kmers[1].hash && verify_revert_sequence(ref, seq_offset, obj)) {
result->offset = seq_offset - obj->seq->length + obj->kmers[1].offset + HASH_SIZE;
result->seq = obj->seq;
result->direction = '-';
- break;
}
-
- i = i->next;
}
-
- result->seq = NULL;
}
int verify_sequence (seq_t * ref, uint seq_offset, hashed_object_t * obj) {
@@ -138,7 +150,6 @@ int kr_align (seq_t * seq, FILE * output) {
/* --- Hash recurence --- */
for (uint idx=0 ; idx<seq->length - HASH_SIZE ; idx++) {
h = hash_decal(h, seq->value[idx+HASH_SIZE-1]);
- printf("%lu\n", h);
// --- Search forward hash ---
search_hash(h, seq, idx, &result);
// Interpret search result
diff --git a/tests/kr_tests.c b/tests/kr_tests.c
index ed5e4dac6633b695109f54234d8289a1fd2f086c..b2d2d9712f23952e600f0ca26c4ba00dd7cfa35a 100644
--- a/tests/kr_tests.c
+++ b/tests/kr_tests.c
@@ -129,17 +129,19 @@ char * fasta_against_sequence_with_overlap_and_rev_comp_test () {
mu_assert("Impossible to execute a kr alignment with the sequence 0", kr_align(sequences, tmp));
destroy_buffer(sequences_buffer);
free(sequences);
+ fclose(tmp);
tmp = fopen(tmp_file, "r");
size_t buff_size = 1024;
char * buffer = malloc(buff_size * sizeof(char));
- mu_assert("0 lines in output", getline(&buffer, &buff_size, tmp) == 0);
+ int lines = getline(&buffer, &buff_size, tmp);
+ mu_assert("0 lines in output", lines != -1);
mu_assert("test allele 2 not found at position 964", strcmp(buffer, "Test_overlapping Must find allele 2x2 but not the 1 and 3 (1 nucleotide missing)\trbsC_S_2\t+\t964\n") == 0);
- mu_assert("not enougth lines in output", getline(&buffer, &buff_size, tmp) == 0);
+ mu_assert("not enougth lines in output", getline(&buffer, &buff_size, tmp) != -1);
mu_assert("test allele 2 not found at position 1929", strcmp(buffer, "Test_overlapping Must find allele 2x2 but not the 1 and 3 (1 nucleotide missing)\trbsC_S_2\t+\t1929\n") == 0);
- mu_assert("not enougth lines in output", getline(&buffer, &buff_size, tmp) == 0);
- mu_assert("test allele 3 not found at position 2895", strcmp(buffer, "Test_overlapping Must find allele 2x2 but not the 1 and 3 (1 nucleotide missing)\trbsC_S_3\t-\t2895\n") == 0);
+ mu_assert("not enougth lines in output", getline(&buffer, &buff_size, tmp) != -1);
+ mu_assert("test allele 3 not found at position 2895", strcmp(buffer, "Test_overlapping Must find allele 2x2 but not the 1 and 3 (1 nucleotide missing)\trbsC_S_3\t-\t3829\n") == 0);
mu_assert("Too much matches on test_seq_overlapp.fasta", getline(&buffer, &buff_size, tmp) != 0);
free(buffer);
@@ -166,13 +168,13 @@ char * rabinkarp_tests() {
char filename[] = "tests/data/data2.fasta";
buffer_t * alleles_buffer = init_buffer(filename);
- uint nb_seq = read_sequences(filename, &alleles, alleles_buffer);
+ nb_seqs = read_sequences(filename, &alleles, alleles_buffer);
/* --- init kmers --- */
FILE * kmers_file = fopen("tests/data/data2.bin", "r");
kmers_init(kmers_file);
- kmers = malloc(2 * nb_seq * sizeof(kmer_t));
- next_kmers(kmers_file, kmers, nb_seq * 2);
+ kmers = malloc(2 * nb_seqs * sizeof(kmer_t));
+ next_kmers(kmers_file, kmers, nb_seqs * 2);
fclose(kmers_file);