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support ALT mapping

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This commit is contained in:
Heng Li
2020-01-21 09:17:50 -05:00
parent d2e14705e7
commit eb3ed6993d
10 changed files with 87 additions and 22 deletions
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minimap.h
+6 -1
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@@ -58,12 +58,14 @@ typedef struct {
char *name; // name of the db sequence
uint64_t offset; // offset in mm_idx_t::S
uint32_t len; // length
uint32_t is_alt;
} mm_idx_seq_t;
typedef struct {
int32_t b, w, k, flag;
uint32_t n_seq; // number of reference sequences
int32_t index;
int32_t n_alt;
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
struct mm_idx_bucket_s *B; // index (hidden)
@@ -91,7 +93,7 @@ typedef struct {
int32_t mlen, blen; // seeded exact match length; seeded alignment block length
int32_t n_sub; // number of suboptimal mappings
int32_t score0; // initial chaining score (before chain merging/spliting)
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, split_inv:1, dummy:7;
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, split_inv:1, is_alt:1, dummy:6;
uint32_t hash;
float div;
mm_extra_t *p;
@@ -127,6 +129,8 @@ typedef struct {
int min_join_flank_sc;
float min_join_flank_ratio;
float alt_diff_frac;
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
@@ -369,6 +373,7 @@ int mm_idx_index_name(mm_idx_t *mi);
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_alt_read(mm_idx_t *mi, const char *fn);
int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);