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r513: merged pre- and post-cigar blen and mlen

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This saves a bit memory and is cleaner.
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Heng Li
2017-10-16 10:55:18 -04:00
parent e6f525edaf
commit adf6cd7f52
5 changed files with 18 additions and 21 deletions
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minimap.h
+1 -3
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@@ -54,8 +54,6 @@ typedef struct {
typedef struct {
uint32_t capacity; // the capacity of cigar[]
int32_t dp_score, dp_max, dp_max2; // DP score; score of the max-scoring segment; score of the best alternate mappings
uint32_t blen; // block length
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;
@@ -71,7 +69,7 @@ typedef struct {
int32_t qs, qe, rs, re; // query start and end; reference start and end
int32_t parent, subsc; // parent==id if primary; best alternate mapping score
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)
int32_t mlen, blen; // seeded exact match length; seeded alignment block length
uint32_t mapq:8, split:2, n_sub:22; // mapQ; split pattern; number of suboptimal mappings
uint32_t sam_pri:1, proper_frag:1, iden_flt:1, pe_thru:1, dummy:29;
uint32_t hash;