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This commit is contained in:
Heng Li 2017-06-23 14:06:00 -04:00
parent 44cdd18de0
commit 326d91deb0
3 changed files with 8 additions and 3 deletions
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2
Makefile
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@ -33,10 +33,12 @@ depend:
# DO NOT DELETE
align.o: minimap.h ksw2.h
bseq.o: bseq.h kseq.h
chain.o: minimap.h mmpriv.h kalloc.h
index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
kalloc.o: kalloc.h
ksw2_extz2_sse.o: ksw2.h
main.o: bseq.h minimap.h mmpriv.h
map.o: kthread.h kvec.h kalloc.h sdust.h minimap.h mmpriv.h bseq.h
misc.o: minimap.h ksort.h

5
align.c
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@ -5,7 +5,7 @@
void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
{
extern unsigned char seq_nt4_table[256];
int i, reg;
int i, k, reg;
uint8_t *qseq0[2];
qseq0[0] = (uint8_t*)kmalloc(km, qlen);
@ -30,6 +30,9 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs];
ret = mm_idx_getseq(mi, rid, rs, re, tseq);
assert(ret > 0);
fprintf(stderr, "===> %d,%d (%s:%d-%d) <===\n", reg, i, 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 < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
}
kfree(km, tseq);
}

4
minimap.h
View File

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