void
verify_node_orig(kg_node_t * node, unsigned kmer_length) {
assert( false && "TODO FIX! REVERSED KMER ENDIANNESS" );
int double_kmer_length = kmer_length << 1;
#ifdef LARGE_KMERS
Kmer mask;
mask.createMask(double_kmer_length);
#else
Kmer mask = (Kmer(1) << double_kmer_length) - 1;
#endif
Kmer kmer = node->kmer;
Kmer rc_kmer = reverseComplement(kmer, kmer_length);
char leftmost_base = (kmer >> (double_kmer_length - 2)) & 0x3;
char rightmost_base = kmer & 0x3;
for (int i = 0 ; i < 4 ; ++ i) {
// check on the left side
kg_node_t * node2 = node->left[i];
int count = node->left_count[i];
if (node2) {
assert (count != 0);
if (count > 0) {
Kmer kmer2 = KMER_PREPEND(kmer, i, double_kmer_length, mask);
assert(kmer2 == node2->kmer);
assert(node2->right[(int)rightmost_base] == node);
assert(node2->right_count[(int)rightmost_base] == count);
} else {
Kmer kmer2 = KMER_APPEND(rc_kmer, i ^ 0x3, double_kmer_length, mask);
assert(kmer2 == node2->kmer);
assert(node2->left[rightmost_base ^ 0x3] == node);
assert(node2->left_count[rightmost_base ^ 0x3] == count);
}
} else {
assert (count == 0);
}
// check on the right side
node2 = node->right[i];
count = node->right_count[i];
if (node2) {
assert (count != 0);
if (count > 0) {
Kmer kmer2 = KMER_APPEND(kmer, i, double_kmer_length, mask);
assert(kmer2 == node2->kmer);
assert(node2->left[(int)leftmost_base] == node);
assert(node2->left_count[(int)leftmost_base] == count);
} else {
Kmer kmer2 = KMER_PREPEND(rc_kmer, i ^ 0x3, double_kmer_length, mask);
assert(kmer2 == node2->kmer);
assert(node2->right[leftmost_base ^ 0x3] == node);
assert(node2->right_count[leftmost_base ^ 0x3] == count);
}
} else {
assert (count == 0);
}
}
}
void
verify_node(kg_node_t * node, unsigned kmer_length) {
assert( false && "TODO FIX! REVERSED KMER ENDIANNESS" );
int double_kmer_length = kmer_length << 1;
Kmer mask = (((Kmer)1) << double_kmer_length) - 1; // a mask with 2*kmer_length bits
Kmer kmer = node->kmer;
Kmer rc_kmer = reverseComplement(kmer, kmer_length); // + node->length - 1);
char leftmost_base = (kmer >> (double_kmer_length - 2)) & 0x3;
char rightmost_base = kmer & 0x3; // (kmer >> ((node->length-1)<<1)) & 0x3;
Kmer lkmer = kmer; // >> ((node->length - 1) << 1); // left kmer
Kmer rrc_kmer = rc_kmer; // >> ((node->length - 1) << 1); // right reverse-complement kmer
for (int i = 0 ; i < 4 ; ++ i) {
// check on the left side
kg_node_t * node2 = node->left[i];
int count = node->left_count[i];
if (node2) {
assert (count != 0);
if (count > 0) {
Kmer kmer2 = KMER_PREPEND(lkmer, i, double_kmer_length, mask);
assert(kmer2 == (node2->kmer & mask));
assert(node2->right[(int)rightmost_base] == node);
assert(node2->right_count[(int)rightmost_base] == count);
} else {
Kmer kmer2 = KMER_APPEND(rc_kmer, i ^ 0x3, double_kmer_length, mask);
assert(kmer2 == node2->kmer); //(node2->kmer >> ((node2->length-1) << 1)));
assert(node2->left[rightmost_base ^ 0x3] == node);
assert(node2->left_count[rightmost_base ^ 0x3] == count);
}
} else {
assert (count == 0);
}
// check on the right side
node2 = node->right[i];
count = node->right_count[i];
if (node2) {
assert (count != 0);
if (count > 0) {
Kmer kmer2 = KMER_APPEND(kmer, i, double_kmer_length, mask);
assert(kmer2 == node2->kmer); // (node2->kmer >> ((node2->length-1) << 1)));
assert(node2->left[(int)leftmost_base] == node);
assert(node2->left_count[(int)leftmost_base] == count);
} else {
Kmer kmer2 = KMER_PREPEND(rrc_kmer, i ^ 0x3, double_kmer_length, mask);
assert(kmer2 == (node2->kmer & mask));
assert(node2->right[leftmost_base ^ 0x3] == node);
assert(node2->right_count[leftmost_base ^ 0x3] == count);
}
} else {
assert (count == 0);
}
}
}
void verify_node(KmerNode * node, KmerGraph *hashtable, unsigned kmer_length)
{
int double_kmer_length = kmer_length << 1;
#ifdef LARGE_KMERS
Kmer mask;
mask.createMask(double_kmer_length);
#else
Kmer mask = (Kmer(1) << double_kmer_length) - 1;
#endif
Kmer kmer = node->kmer;
Kmer rc_kmer = reverseComplement(kmer, kmer_length);
char rightmost_base = KMER_GET_TAIL_BASE(kmer, kmer_length);
char leftmost_base = KMER_GET_HEAD_BASE(kmer, kmer_length);
KmerNode *node2;
for (int i = 0 ; i < 4 ; ++ i) {
// check on the left side
int count = node->left_count[i];
int color = node->left_color[i];
assert( color == 0 || count != 0 ); // count must be non-zero if color is non-zero
if (color == 0) {
if (count > 0) {
Kmer kmer2 = KMER_PREPEND(kmer, i, double_kmer_length, mask);
node2 = hashtable->findNode(canonicalKmer(kmer2, kmer_length));
assert( node2 != NULL );
assert(cnorm(node2->right_count[static_cast<int>(rightmost_base)]) == cnorm(count));
assert(node2->right_color[static_cast<int>(rightmost_base)] == 0);
} else if (count < 0) {
Kmer kmer2 = KMER_APPEND(rc_kmer, i ^ 0x3, double_kmer_length);
node2 = hashtable->findNode(canonicalKmer(kmer2, kmer_length));
assert( node2 != NULL );
assert(cnorm(node2->left_count[static_cast<int>( COMPLEMENT(rightmost_base) )]) == cnorm(count));
assert(node2->left_color[static_cast<int>( COMPLEMENT(rightmost_base) )] == 0);
}
}
// check on the right side
count = node->right_count[i];
color = node->right_color[i];
assert( color == 0 || count != 0 ); // count must be non-zero if color is non-zero
if (color == 0) {
if (count > 0) {
Kmer kmer2 = KMER_APPEND(kmer, i, double_kmer_length);
node2 = hashtable->findNode(canonicalKmer(kmer2, kmer_length));
assert( node2 != NULL );
assert(cnorm(node2->left_count[static_cast<int>(leftmost_base)]) == cnorm(count));
assert(node2->left_color[static_cast<int>(leftmost_base)] == 0);
} else if (count < 0) {
Kmer kmer2 = KMER_PREPEND(rc_kmer, i ^ 0x3, double_kmer_length, mask);
node2 = hashtable->findNode(canonicalKmer(kmer2, kmer_length));
assert( node2 != NULL );
assert(cnorm(node2->right_count[static_cast<int>( COMPLEMENT(leftmost_base) )]) == cnorm(count));
assert(node2->right_color[static_cast<int>( COMPLEMENT(leftmost_base) )] == 0);
}
}
}
}