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r935: fixed a cigar like 5I6D7I; resolved #392

This commit is contained in:
Heng Li 2019-04-30 21:35:24 -04:00
parent 49c6d83a8e
commit 69af86657e
2 changed files with 20 additions and 1 deletions
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19
align.c
View File

@ -123,6 +123,25 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
}
}
assert(qoff == r->qe - r->qs && toff == r->re - r->rs);
for (k = 0; k < p->n_cigar - 2; ++k) { // fix CIGAR like 5I6D7I
if ((p->cigar[k]&0xf) > 0 && (p->cigar[k]&0xf) + (p->cigar[k+1]&0xf) == 3) {
uint32_t l, s[3] = {0,0,0};
for (l = k; l < p->n_cigar; ++l) { // count number of adjacent I and D
uint32_t op = p->cigar[l]&0xf;
if (op == 1 || op == 2 || p->cigar[l]>>4 == 0)
s[op] += p->cigar[l] >> 4;
else break;
}
if (s[1] > 0 && s[2] > 0 && l - k > 2) { // turn to a single I and a single D
p->cigar[k] = s[1]<<4|1;
p->cigar[k+1] = s[2]<<4|2;
for (k += 2; k < l; ++k)
p->cigar[k] &= 0xf;
to_shrink = 1;
}
k = l;
}
}
if (to_shrink) { // squeeze out zero-length operations
int32_t l = 0;
for (k = 0; k < p->n_cigar; ++k) // squeeze out zero-length operations

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.16-r934-dirty"
#define MM_VERSION "2.16-r935-dirty"
#ifdef __linux__
#include <sys/resource.h>