#include <string.h>
#include "bam.h"
#include "bam2bcf.h"
-#include "ksort.h"
#include "kaln.h"
#include "kprobaln.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
for (k = 0; k < c->n_cigar; ++k) {
int op = cigar[k] & BAM_CIGAR_MASK;
int l = cigar[k] >> BAM_CIGAR_SHIFT;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
if (c->pos > tpos) return y;
if (x + l > tpos) {
*_tpos = tpos;
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash)
{
- extern void ks_introsort_uint32_t(int, uint32_t*);
int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query, **ref_sample;
if (j > max_rd_len) max_rd_len = j;
}
}
+ // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+ // check the number of N's in the sequence and skip places where half or more reference bases are Ns.
+ int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+ if ( nN*2>i ) return -1;
+
ks_introsort(uint32_t, m, aux);
// squeeze out identical types
for (i = 1, n_types = 1; i < m; ++i)
if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
free(aux); return -1;
}
+ if (n_types >= 64) {
+ free(aux);
+ if (bam_verbose >= 2)
+ fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
+ return -1;
+ }
types = (int*)calloc(n_types, sizeof(int));
t = 0;
types[t++] = aux[0] - MINUS_CONST;
for (t = 0; t < n_types; ++t)
if (types[t] == 0) break;
ref_type = t; // the index of the reference type (0)
- assert(n_types < 64);
}
{ // calculate left and right boundary
left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
for (k = 0; k < b->core.n_cigar; ++k) {
int op = cigar[k]&0xf;
int j, l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (j = 0; j < l; ++j)
if (x + j >= left && x + j < right)
cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;