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implemented in exts; testing is the next

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Heng Li
2019-04-28 16:47:12 -04:00
parent cdc730d573
commit be171aa2dc
8 changed files with 37 additions and 20 deletions
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minimap.h
+2 -1
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@@ -128,6 +128,7 @@ typedef struct {
int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
int sc_ambi; // score when one or both bases are "N"
int noncan; // cost of non-canonical splicing sites
int junc_bonus;
int zdrop, zdrop_inv; // break alignment if alignment score drops too fast along the diagonal
int end_bonus;
int min_dp_max; // drop an alignment if the score of the max scoring segment is below this threshold
@@ -367,7 +368,7 @@ int mm_idx_name2id(const mm_idx_t *mi, const char *name);
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
int mm_idx_bed_read(mm_idx_t *mi, const char *fn);
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, int32_t strand, int8_t *s);
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);
// deprecated APIs for backward compatibility
void mm_mapopt_init(mm_mapopt_t *opt);