void checksuflinks(Suffixarray *s, Uint i, Uint j){
Uint k, childlcp, suflcp, *space = NULL;
PairUint* child, childsuf;
Container *children;
// ignore singletons as initial input
if (i == j){
return;
}
children = getChildintervals(space, s, i, j, 0);
for (k = 0; k < bl_containerSize(children); k++){
child = (PairUint *) bl_containerGet(children, k);
// exclude singletons
if (child->a == child->b){
return;
}
// check suflink of child
childlcp = getlcpval(s, child->a, child->b);
childsuf = getSuflink(s, child->a, child->b);
suflcp = getlcpval(s, childsuf.a, childsuf.b);
if (childlcp != suflcp + 1){
DBG("suf[%u, %u, %u]=[%u, %u, %u]\n", child->a, child->b, childlcp,
childsuf.a, childsuf.b, suflcp);
}
// recursively check all children of child
checksuflinks(s, child->a, child->b);
}
bl_containerDestruct(children, NULL);
free(children);
}
void FragmentList::freeFragList(Container* frags) {
for (uint32_t i = 0; i < bl_containerSize(frags); i++){
slmatch_t *sl = (slmatch_t *) bl_containerGet(frags, i);
if (sl->chain != nullptr){
std::cerr << "still at least one chain not freed before end: " << i << "\n";
exit(-1);
bl_slchainDestruct(sl->chain);
free(sl->chain);
}
}
bl_containerDestruct(frags, bl_slmatchDestruct);
free(frags);
}
void suffix_mng_free(suffix_mng_t *p) {
if (p) {
if (p->suffix_lists) {
for (int i = 0; i < p->num_chroms; i++) {
if (p->suffix_lists[i]) {
linked_list_free(p->suffix_lists[i], (void *)seed_free);
}
}
free(p->suffix_lists);
}
if (p->subject){
for (int i = 0; i < bl_containerSize(p->subject); i++) {
free(*(char **) bl_containerGet(p->subject, i));
}
bl_containerDestruct(p->subject, NULL);
free(p->subject);
}
free(p);
}
}
void
kmismatch(void *space,
Suffixarray *s,
fasta_t *reads,
Uint k,
Uint* counter,
Uint rep_type,
unsigned char silent,
FILE *dev)
{
Uint i, curlen;
char *buffer, *curseq;
branch_t *V;
Gmap map;
Uint noofmatches=0;
gread_t read;
Container C;
pthread_mutex_t *mtx=NULL;
if (counter == NULL) {
initProgressBarVT();
} else {
mtx = &mutex2;
}
initGmap(&map, s->seq, 1);
for (i=0; i < reads->noofseqs; i++) {
noofmatches = 0;
initRead(&read, reads->seqs[i]);
setReads(&map, &read, 1);
if (!silent) {
if (mtx == NULL) {
progressBarVT("reads matched.", reads->noofseqs, i, 25);
} else {
(*counter)++;
}
}
curseq = reads->seqs[i]->sequence;
curlen = reads->seqs[i]->length;
V=kmis(space, s, curseq, curlen, k, &noofmatches);
if(noofmatches) {
bl_containerInit(&C, 100, sizeof(gmatch_t));
branch2match(s, &C, V, noofmatches);
setMatches(&read, (gmatch_t*)C.contspace,
bl_containerSize(&C), PLUSSTRAND);
reportMatch(dev, &map, rep_type, 0, mtx, curlen, curlen);
bl_containerDestruct(&C, NULL);
FREEMEMORY(space, V);
}
initRead(&read, reads->seqs[i]);
setReads(&map, &read, 1);
buffer = charDNAcomplement(space, curseq, curlen);
V=kmis(space, s, buffer, curlen, k, &noofmatches);
if(noofmatches) {
bl_containerInit(&C, 100, sizeof(gmatch_t));
branch2match(s, &C, V, noofmatches);
setMatches(&read, (gmatch_t*)C.contspace,
bl_containerSize(&C), MINUSSTRAND);
reportMatch(dev, &map, rep_type, 0, mtx, curlen, curlen);
bl_containerDestruct(&C, NULL);
FREEMEMORY(space, V);
}
FREEMEMORY(space, buffer);
}
return;
}
