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r248: contained reads not handled properly

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Heng Li
2020-05-03 00:27:53 -04:00
parent 7f6725ead3
commit 331e437c72
2 changed files with 16 additions and 8 deletions
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CommandLines.h
+1 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.5-dirty-r247"
#define HA_VERSION "0.5-dirty-r248"
#define VERBOSE 0
anchor.cpp
+15 -7
View File
@@ -50,6 +50,13 @@ uint64_t ha_abuf_mem(const ha_abuf_t *ab)
return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(ha_mz1_t) + sizeof(seed1_t)) + sizeof(ha_abuf_t);
}
static int ha_ov_type(const overlap_region *r, uint32_t len)
{
if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 2; // containing a shorter read
else return r->x_pos_s == 0? 0 : 1;
}
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain)
{
extern void *ha_flt_tab;
@@ -137,19 +144,20 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
#endif
if ((int)overlap_list->length > max_n_chain) {
int32_t n[2], s[2];
n[0] = n[1] = 0, s[0] = s[1] = 0;
uint32_t len = Get_READ_LENGTH(R_INF, rid);
int32_t w, n[3], s[3];
n[0] = n[1] = n[2] = 0, s[0] = s[1] = s[2] = 0;
for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
const overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
++n[dir];
if ((int)n[dir] == max_n_chain) s[dir] = r->shared_seed;
w = ha_ov_type(r, len);
++n[w];
if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
}
if (s[0] > 0 || s[1] > 0) {
for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
if (r->shared_seed > s[dir]) {
w = ha_ov_type(r, len);
if (r->shared_seed > s[w]) {
if ((uint32_t)k != i) {
overlap_region t;
t = overlap_list->list[k];