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;
return max_i - pos;
}
+/*
+ * @n: number of samples
+ */
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)
{
if (s == n) return -1; // there is no indel at this position.
for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
{ // find out how many types of indels are present
- int m, n_alt = 0, n_tot = 0;
+ bca->max_support = bca->max_frac = 0;
+ int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
uint32_t *aux;
aux = calloc(N + 1, 4);
m = max_rd_len = 0;
aux[m++] = MINUS_CONST; // zero indel is always a type
for (s = 0; s < n; ++s) {
+ int na = 0, nt = 0;
for (i = 0; i < n_plp[s]; ++i) {
const bam_pileup1_t *p = plp[s] + i;
if (rghash == 0 || p->aux == 0) {
- ++n_tot;
+ ++nt;
if (p->indel != 0) {
- ++n_alt;
+ ++na;
aux[m++] = MINUS_CONST + p->indel;
}
}
j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
if (j > max_rd_len) max_rd_len = j;
}
+ float frac = (float)na/nt;
+ if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
+ indel_support_ok = 1;
+ if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
+ n_alt += na;
+ n_tot += nt;
}
+ // 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 ) { free(aux); return -1; }
+
ks_introsort(uint32_t, m, aux);
// squeeze out identical types
for (i = 1, n_types = 1; i < m; ++i)
if (aux[i] != aux[i-1]) ++n_types;
- if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
- free(aux); return -1;
+ // Taking totals makes it hard to call rare indels
+ if ( !bca->per_sample_flt )
+ indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
+ if ( n_types == 1 || !indel_support_ok ) { // 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;
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;
* reduces the power because sometimes, substitutions caused by
* indels are not distinguishable from true mutations. Multiple
* sequence realignment helps to increase the power.
+ *
+ * Masks mismatches present in at least 70% of the reads with 'N'.
*/
{ // construct per-sample consensus
int L = right - left + 1, max_i, max2_i;
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;
if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
if (max_i >= 0) r[max_i] = 15;
if (max2_i >= 0) r[max2_i] = 15;
-// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+ //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
}
free(ref0); free(cns);
}
}
}
// construct the consensus sequence
- max_ins = types[n_types - 1]; // max_ins is at least 0
+ max_ins = types[n_types - 1]; // max_ins is at least 0
if (max_ins > 0) {
- int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
+ int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
// count the number of occurrences of each base at each position for each type of insertion
for (t = 0; t < n_types; ++t) {
if (types[t] > 0) {
uint8_t *seq = bam1_seq(p->b);
for (k = 1; k <= p->indel; ++k) {
int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
- if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
+ assert(c<5);
+ ++inscns_aux[(t*max_ins+(k-1))*5 + c];
}
}
}
inscns = calloc(n_types * max_ins, 1);
for (t = 0; t < n_types; ++t) {
for (j = 0; j < types[t]; ++j) {
- int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
- for (k = 0; k < 4; ++k)
+ int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+ for (k = 0; k < 5; ++k)
if (ia[k] > max)
max = ia[k], max_k = k;
inscns[t*max_ins + j] = max? max_k : 4;
+ if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
}
}
free(inscns_aux);
projects / samtools.git / blobdiff