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Merge branch 'master' into utec

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This commit is contained in:
Heng Li
2021-07-16 13:32:47 -04:00
parent 28a37a017a 581f2d7123
commit b046052d82
39 changed files with 2143 additions and 531 deletions
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minimap.h
+22 -9
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@@ -36,8 +36,9 @@
#define MM_F_NO_END_FLT 0x10000000
#define MM_F_HARD_MLEVEL 0x20000000
#define MM_F_SAM_HIT_ONLY 0x40000000
#define MM_F_QSTRAND (0x80000000LL)
#define MM_F_NO_INV (0x100000000LL)
#define MM_F_RMQ 0x80000000LL
#define MM_F_QSTRAND (0x100000000LL)
#define MM_F_NO_INV (0x200000000LL)
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2
@@ -47,6 +48,18 @@
#define MM_MAX_SEG 255
#define MM_CIGAR_MATCH 0
#define MM_CIGAR_INS 1
#define MM_CIGAR_DEL 2
#define MM_CIGAR_N_SKIP 3
#define MM_CIGAR_SOFTCLIP 4
#define MM_CIGAR_HARDCLIP 5
#define MM_CIGAR_PADDING 6
#define MM_CIGAR_EQ_MATCH 7
#define MM_CIGAR_X_MISMATCH 8
#define MM_CIGAR_STR "MIDNSHP=XB"
#ifdef __cplusplus
extern "C" {
#endif
@@ -115,22 +128,22 @@ typedef struct {
int max_qlen; // max query length
int bw; // bandwidth
int bw, bw_long; // bandwidth
int max_gap, max_gap_ref; // break a chain if there are no minimizers in a max_gap window
int max_frag_len;
int max_chain_skip, max_chain_iter;
int min_cnt; // min number of minimizers on each chain
int min_chain_score; // min chaining score
float chain_gap_scale;
int rmq_size_cap, rmq_inner_dist;
int rmq_rescue_size;
float rmq_rescue_ratio;
float mask_level;
int mask_len;
float pri_ratio;
int best_n; // top best_n chains are subjected to DP alignment
int max_join_long, max_join_short;
int min_join_flank_sc;
float min_join_flank_ratio;
float alt_drop;
int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
@@ -147,9 +160,9 @@ typedef struct {
int pe_ori, pe_bonus;
float mid_occ_frac; // only used by mm_mapopt_update(); see below
int32_t min_mid_occ;
int32_t min_mid_occ, max_mid_occ;
int32_t mid_occ; // ignore seeds with occurrences above this threshold
int32_t max_occ;
int32_t max_occ, max_max_occ, occ_dist;
int64_t mini_batch_size; // size of a batch of query bases to process in parallel
int64_t max_sw_mat;