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sequence retrieval working

This commit is contained in:
Heng Li 2017-06-23 14:11:56 -04:00
parent 326d91deb0
commit 9cd313eae1
2 changed files with 3 additions and 3 deletions
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2
align.c
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@ -30,7 +30,7 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs]; qseq = &qseq0[rev][qs];
ret = mm_idx_getseq(mi, rid, rs, re, tseq); ret = mm_idx_getseq(mi, rid, rs, re, tseq);
assert(ret > 0); assert(ret > 0);
fprintf(stderr, "===> %d,%d (%s:%d-%d) <===\n", reg, i, mi->seq[rid].name, rs, re); fprintf(stderr, "===> [%d,%d] %d-%d %c (%s:%d-%d) <===\n", reg, i, qs, qe, "+-"[rev], mi->seq[rid].name, rs, re);
for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr); for (k = 0; k < re - rs; ++k) fputc("ACGTN"[tseq[k]], stderr); fputc('\n', stderr);
for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr); for (k = 0; k < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
} }

4
minimap.h
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@ -74,8 +74,8 @@ typedef struct mm_tbuf_s mm_tbuf_t;
struct bseq_file_s; struct bseq_file_s;
#define mm_seq4_set(s, i, c) ((s)[(i)>>4] |= (uint32_t)(c) << (((i)&7)<<2)) #define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
#define mm_seq4_get(s, i) ((s)[(i)>>4] >> (((i)&7)<<2) & 0xf) #define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
#ifdef __cplusplus #ifdef __cplusplus
extern "C" { extern "C" {