fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-06 17:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r512: option to filter poorly aligned reads

Browse Source
This commit is contained in:
Heng Li
2017-10-16 10:38:22 -04:00
parent 858213d513
commit e6f525edaf
8 changed files with 131 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files
minimap.h
+4 -1
View File
@@ -58,6 +58,8 @@ typedef struct {
uint32_t n_diff; // number of differences, including ambiguous bases
uint32_t n_ambi:30, trans_strand:2; // number of ambiguous bases; transcript strand: 0 for unknown, 1 for +, 2 for -
uint32_t n_cigar; // number of cigar operations in cigar[]
float n_diff2;
uint32_t blen2;
uint32_t cigar[];
} mm_extra_t;
@@ -71,7 +73,7 @@ typedef struct {
int32_t as; // offset in the a[] array (for internal uses only)
int32_t fuzzy_mlen, fuzzy_blen; // seeded exact match length; seeded alignment block length (approximate)
uint32_t mapq:8, split:2, n_sub:22; // mapQ; split pattern; number of suboptimal mappings
uint32_t sam_pri:1, proper_frag:1, dummy:30;
uint32_t sam_pri:1, proper_frag:1, iden_flt:1, pe_thru:1, dummy:29;
uint32_t hash;
mm_extra_t *p;
} mm_reg1_t;
@@ -98,6 +100,7 @@ typedef struct {
float mask_level;
float pri_ratio;
int best_n; // top best_n chains are subjected to DP alignment
float min_iden;
int max_join_long, max_join_short;
int min_join_flank_sc;