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update polishing

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chhylp123
2020-10-18 17:59:31 -04:00
parent 753ea81194
commit 9d4e3b3283
5 changed files with 417 additions and 567 deletions
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Correct.h
+14
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@@ -1175,6 +1175,20 @@ long long get_affine_gap_score(overlap_region* ovc, UC_Read* g_read, UC_Read* ov
uint8_t* y_num, uint64_t EstimateXOlen, uint64_t EstimateYOlen);
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u8_warp* k_flag, float hp_rate, int rlen, FILE* fp);
inline int if_exact_match(char* x, long long xLen, char* y, long long yLen, long long xBeg, long long xEnd, long long yBeg, long long yEnd)
{
long long overlapLen = xEnd - xBeg + 1;
if(yEnd - yBeg + 1 == overlapLen)
{
if(memcmp(x+xBeg, y+yBeg, overlapLen)==0) return 1;
}
return 0;
}
#define FORWARD_KSW 0
#define BACKWARD_KSW 1
#define MATCH_SCORE_KSW 2