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r466: detect multi-part index more smartly

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though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
This commit is contained in:
Heng Li
2017-10-04 17:32:58 -04:00
parent 1554149158
commit 7d50e646dd
7 changed files with 40 additions and 39 deletions
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mmpriv.h
+1 -2
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@@ -54,8 +54,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
void mm_write_sam_SQ(const mm_idx_t *idx);
void mm_write_sam_hdr_no_SQ(const char *rg, const char *ver, int argc, char *argv[]);
void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);