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r227: use local alignment for INV alignment

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Heng Li
2017-07-29 17:40:53 -04:00
parent da3db3c095
commit d08b7a0c51
5 changed files with 179 additions and 21 deletions
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ksw2.h
+3
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@@ -67,6 +67,9 @@ int ksw_gg(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *ta
int ksw_gg2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_);
int ksw_gg2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_);
void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, const int8_t *mat);
int ksw_ll_i16(void *q, int tlen, const uint8_t *target, int gapo, int gape, int *qe, int *te);
#ifdef __cplusplus
}
#endif