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updated mappy and example.c

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This commit is contained in:
Heng Li
2017-10-16 11:15:07 -04:00
parent adf6cd7f52
commit b24c9c90c7
6 changed files with 28 additions and 15 deletions
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example.c
+1 -2
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@@ -43,8 +43,7 @@ int main(int argc, char *argv[])
mm_reg1_t *r = &reg[j];
assert(r->p); // with MM_F_CIGAR, this should not be NULL
printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re,
r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen, r->mapq);
printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq);
for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
putchar('\n');