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smaller cigar size

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chhylp123
2022-05-12 18:31:31 -04:00
parent a2198891e7
commit 832e43fe3b
3 changed files with 21 additions and 17 deletions
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Correct.cpp
+14 -2
View File
@@ -1804,10 +1804,13 @@ inline int move_gap_greedy(char* path, int path_i, int path_length, char* x, int
inline void generate_cigar(char* path, int path_length, window_list *idx, window_list_alloc *res, int* start, int* end, unsigned int* old_error,
char* x, int x_len, char* y)
{
// uint8_t debug_c; uint32_t debug_c_len;
idx->cidx = res->c.n;
if ((*old_error) == 0) {
push_cigar_cell(res, 0, idx->x_end + 1 - idx->x_start);
idx->clen = res->c.n - idx->cidx;
// get_cigar_cell(idx, res, idx->clen-1, &debug_c, &debug_c_len);
// assert(debug_c==0 && debug_c_len==(idx->x_end + 1 - idx->x_start));
return;
}
@@ -1887,7 +1890,11 @@ inline void generate_cigar(char* path, int path_length, window_list *idx, window
pre_c = 5; pre_cl = 0;
for (i = path_length - 1; i >= 0; i--) {
if (pre_c != path[i]) {
if (pre_cl != 0) push_cigar_cell(res, pre_c, pre_cl);
if (pre_cl != 0) {
push_cigar_cell(res, pre_c, pre_cl);
// get_cigar_cell(idx, res, res->c.n - idx->cidx - 1, &debug_c, &debug_c_len);
// assert(debug_c==pre_c && debug_c_len==pre_cl);
}
pre_c = path[i]; pre_cl = 1;
}
else {
@@ -1895,7 +1902,12 @@ inline void generate_cigar(char* path, int path_length, window_list *idx, window
}
}
if (pre_cl != 0) push_cigar_cell(res, pre_c, pre_cl);
if (pre_cl != 0) {
push_cigar_cell(res, pre_c, pre_cl);
// get_cigar_cell(idx, res, res->c.n - idx->cidx -1, &debug_c, &debug_c_len);
// assert(debug_c==pre_c && debug_c_len==pre_cl);
}
idx->clen = res->c.n - idx->cidx;
// if(verify_cigar(x, x_len, y, (*end) - (*start) + 1, &(result->cigar), *old_error))
// {
Correct.h
+4 -4
View File
@@ -1251,14 +1251,14 @@ inline int if_exact_match(char* x, long long xLen, char* y, long long yLen, long
inline void get_cigar_cell(window_list *idx, window_list_alloc *cc, uint32_t i, uint8_t *c, uint32_t *len)
{
uint32_t p = cc->c.a[idx->cidx+i];
(*c) = (uint8_t)(p>>30); (*len) = (p<<2)>>2;
uint16_t p = cc->c.a[idx->cidx+i];
(*c) = (uint8_t)(p>>14); (*len) = (p&((uint16_t)0x3fff));
}
inline void push_cigar_cell(window_list_alloc *res, uint8_t c, uint32_t len)
{
uint32_t p = c; p <<= 30; p += len;
kv_push(uint32_t, res->c, p);
uint16_t p = c; p <<= 14; p += (uint16_t)len;
kv_push(uint16_t, res->c, p);
}
#define FORWARD_KSW 0
Hash_Table.h
+3 -11
View File
@@ -44,29 +44,21 @@ typedef struct
uint64_t end_pos;
} k_mer_pos_list;
// typedef struct
// {
// int C_L[CIGAR_MAX_LENGTH];
// char C_C[CIGAR_MAX_LENGTH];
// int length;
// } CIGAR;
typedef struct
{
///the begining and end of a window, instead of the whole overlap
int32_t x_start, x_end;
int32_t y_start, y_end;
int32_t extra_begin, extra_end;
int32_t error, error_threshold;
int16_t extra_begin, extra_end;
int16_t error, error_threshold;
uint32_t cidx, clen;
//CIGAR cigar;
} window_list;
typedef struct
{
size_t n, m;
window_list *a;
kvec_t(uint32_t) c;
kvec_t(uint16_t) c;
} window_list_alloc;
typedef struct