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for v0.14

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chhylp123
2021-02-09 13:00:23 -05:00
parent fda13cb0e4
commit 8467d58ef1
7 changed files with 2928 additions and 925 deletions
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Overlaps.h
+10 -4
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@@ -21,6 +21,7 @@
#define PRIMARY_LABLE 0
#define ALTER_LABLE 1
#define HAP_LABLE 2
#define FAKE_LABLE 4
#define TRIO_THRES 0.9
#define DOUBLE_CHECK_THRES 0.1
#define FINAL_DOUBLE_CHECK_THRES 0.2
@@ -106,6 +107,11 @@ typedef struct {
uint8_t no_l_indel;
} asg_arc_t;
typedef struct {
size_t n, m;
asg_arc_t* a;
} kv_asg_arc_t;
typedef struct {
uint32_t len:31, circ:1; // len: length of the unitig; circ: circular if non-zero
@@ -468,7 +474,7 @@ typedef struct {
void init_R_to_U(R_to_U* x, uint64_t len);
void destory_R_to_U(R_to_U* x);
void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig);
void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig, uint8_t* flag);
void get_R_to_U(R_to_U* x, uint32_t rID, uint32_t* uID, uint32_t* is_Unitig);
void transfor_R_to_U(R_to_U* x);
void debug_utg_graph(ma_ug_t *ug, asg_t* read_g, int require_equal_nv, int test_tangle);
@@ -762,7 +768,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
for (b_max.readI = 0; b_max.readI < node_max->n; b_max.readI++)
{
qn = (node_max->a[b_max.readI]>>33);
set_R_to_U(ruIndex, qn, (b_max.b_0->b.a[b_max.untigI]>>1), 1);
set_R_to_U(ruIndex, qn, (b_max.b_0->b.a[b_max.untigI]>>1), 1, &(read_sg->seq[qn].c));
}
}
/*****************************label all unitigs****************************************/
@@ -819,7 +825,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, uint32_t stops_threshold)
for (b_max.untigI = 0; b_max.untigI < b_max.b_0->b.n; b_max.untigI++)
{
qn = (b_max.b_0->b.a[b_max.untigI]>>1);
set_R_to_U(ruIndex, qn, 1, 1);
set_R_to_U(ruIndex, qn, 1, 1, &(read_sg->seq[qn].c));
}
/*****************************label all reads****************************************/
@@ -1043,7 +1049,7 @@ typedef struct{
double weight;
uint32_t uID:31, del:1;
uint64_t dis;
uint64_t occ;
uint64_t occ:63, scaff:1;
///uint32_t enzyme;
} hc_edge;