#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
-#define MIN_SUPPORT_COEF 500
void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
{
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;
+ 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;
+ char *inscns = 0, *ref2, *query, **ref_sample;
khash_t(rg) *hash = (khash_t(rg)*)rghash;
if (ref == 0 || bca == 0) return -1;
// mark filtered reads
// 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 || n_alt * MIN_SUPPORT_COEF < n_tot) { // no indels or too few supporting reads
+ if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
free(aux); return -1;
}
types = (int*)calloc(n_types, sizeof(int));
if (ref[i] == 0) break;
right = i;
}
+ /* The following block fixes a long-existing flaw in the INDEL
+ * calling model: the interference of nearby SNPs. However, it also
+ * reduces the power because sometimes, substitutions caused by
+ * indels are not distinguishable from true mutations. Multiple
+ * sequence realignment helps to increase the power.
+ */
+ { // construct per-sample consensus
+ int L = right - left + 1, max_i, max2_i;
+ uint32_t *cns, max, max2;
+ char *ref0, *r;
+ ref_sample = calloc(n, sizeof(void*));
+ cns = calloc(L, 4);
+ ref0 = calloc(L, 1);
+ for (i = 0; i < right - left; ++i)
+ ref0[i] = bam_nt16_table[(int)ref[i+left]];
+ for (s = 0; s < n; ++s) {
+ r = ref_sample[s] = calloc(L, 1);
+ memset(cns, 0, sizeof(int) * L);
+ // collect ref and non-ref counts
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ bam1_t *b = p->b;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ int x = b->core.pos, y = 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) {
+ 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;
+ x += l; y += l;
+ } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ }
+ }
+ // determine the consensus
+ for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+ max = max2 = 0; max_i = max2_i = -1;
+ for (i = 0; i < right - left; ++i) {
+ if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+ else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+ }
+ if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+ 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);
+ }
+ free(ref0); free(cns);
+ }
{ // the length of the homopolymer run around the current position
int c = bam_nt16_table[(int)ref[pos + 1]];
if (c == 15) l_run = 1;
free(inscns_aux);
}
// compute the likelihood given each type of indel for each read
- ref2 = calloc(right - left + max_ins + 2, 1);
+ max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+ ref2 = calloc(max_ref2, 1);
query = calloc(right - left + max_rd_len + max_ins + 2, 1);
score1 = calloc(N * n_types, sizeof(int));
score2 = calloc(N * n_types, sizeof(int));
else ir = est_indelreg(pos, ref, -types[t], 0);
if (ir > bca->indelreg) bca->indelreg = ir;
// fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
- // write ref2
- for (k = 0, j = left; j <= pos; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- if (types[t] <= 0) j += -types[t];
- else for (l = 0; l < types[t]; ++l)
- ref2[k++] = inscns[t*max_ins + l];
- if (types[0] < 0) { // mask deleted sequences to avoid a particular error in the model.
- int jj, tmp = types[t] >= 0? -types[0] : -types[0] + types[t];
- for (jj = 0; jj < tmp && j < right && ref[j]; ++jj, ++j)
- ref2[k++] = 4;
- }
- for (; j < right && ref[j]; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- if (j < right) right = j;
- // align each read to ref2
+ // realignment
for (s = K = 0; s < n; ++s) {
+ // write ref2
+ for (k = 0, j = left; j <= pos; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ if (types[t] <= 0) j += -types[t];
+ else for (l = 0; l < types[t]; ++l)
+ ref2[k++] = inscns[t*max_ins + l];
+ for (; j < right && ref[j]; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ for (; k < max_ref2; ++k) ref2[k] = 4;
+ if (j < right) right = j;
+ // align each read to ref2
for (i = 0; i < n_plp[s]; ++i, ++K) {
bam_pileup1_t *p = plp[s] + i;
- int qbeg, qend, tbeg, tend, sc;
+ int qbeg, qend, tbeg, tend, sc, kk;
uint8_t *seq = bam1_seq(p->b);
+ uint32_t *cigar = bam1_cigar(p->b);
+ if (p->b->core.flag&4) continue; // unmapped reads
+ // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
+ for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+ if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
+ if (kk < p->b->core.n_cigar) continue;
// FIXME: the following skips soft clips, but using them may be more sensitive.
// determine the start and end of sequences for alignment
qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
// pick the smaller between indelQ1 and indelQ2
indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
- p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
+ if (indelQ > 255) indelQ = 255;
+ if (seqQ > 255) seqQ = 255;
+ p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
-// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ);
+// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
}
}
// determine bca->indel_types[] and bca->inscns
}
free(score1); free(score2);
// free
+ for (i = 0; i < n; ++i) free(ref_sample[i]);
+ free(ref_sample);
free(types); free(inscns);
return n_alt > 0? 0 : -1;
}
projects / samtools.git / blobdiff