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Heng Li
2017-06-23 19:31:23 -04:00
parent d75b5b4e8a
commit 7ed26a4857
1 changed files with 3 additions and 3 deletions
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align.c
+3 -3
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@@ -113,7 +113,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
#if 1
#if 0
fprintf(stderr, "===> [%d] %d-%d %c (%s:%d-%d) <===\n", 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 < qe - qs; ++k) fputc("ACGTN"[qseq[k]], stderr); fputc('\n', stderr);
@@ -123,14 +123,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
} else {
mm_append_cigar(r, ez->n_cigar, ez->cigar);
}
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
//for (k = 0; k < r->cigar->n; ++k) fprintf(stderr, "%d%c", r->cigar->cigar[k]>>4, "MID"[r->cigar->cigar[k]&0xf]); fputc('\n', stderr);
rs = re, qs = qe;
}
}
if (i == r->cnt) {
}
// fprintf(stderr, "%d,%d\n", rs1, qs1); for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
for (i = 0; i < r->cigar->n; ++i) fprintf(stderr, "%d%c", r->cigar->cigar[i]>>4, "MID"[r->cigar->cigar[i]&0xf]); fputc('\n', stderr);
kfree(km, tseq);
}