#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
-#define MAX_SCORE 90
+#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, *score, N, K, l_run, ref_type, n_alt;
+ int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2;
+ int N, K, l_run, ref_type, n_alt;
char *inscns = 0, *ref2, *query;
khash_t(rg) *hash = (khash_t(rg)*)rghash;
if (ref == 0 || bca == 0) return -1;
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;
+ int m, n_alt = 0, n_tot = 0;
uint32_t *aux;
aux = calloc(N + 1, 4);
m = max_rd_len = 0;
for (s = 0; s < n; ++s) {
for (i = 0; i < n_plp[s]; ++i) {
const bam_pileup1_t *p = plp[s] + i;
- if (p->indel != 0 && (rghash == 0 || p->aux == 0))
- aux[m++] = MINUS_CONST + p->indel;
+ if (rghash == 0 || p->aux == 0) {
+ ++n_tot;
+ if (p->indel != 0) {
+ ++n_alt;
+ 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;
}
// 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) { // no indels
+ if (n_types == 1 || n_alt * MIN_SUPPORT_COEF < n_tot) { // no indels or too few supporting reads
free(aux); return -1;
}
types = (int*)calloc(n_types, sizeof(int));
// compute the likelihood given each type of indel for each read
ref2 = calloc(right - left + max_ins + 2, 1);
query = calloc(right - left + max_rd_len + max_ins + 2, 1);
- score = calloc(N * n_types, sizeof(int));
+ score1 = calloc(N * n_types, sizeof(int));
+ score2 = calloc(N * n_types, sizeof(int));
bca->indelreg = 0;
for (t = 0; t < n_types; ++t) {
int l, ir;
- ka_param2_t ap = ka_param2_qual;
- ap.band_width = abs(types[t]) + 3;
+ kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
+ apf1.bw = apf2.bw = abs(types[t]) + 3;
// compute indelreg
if (types[t] == 0) ir = 0;
else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
bam_pileup1_t *p = plp[s] + i;
int qbeg, qend, tbeg, tend, sc;
uint8_t *seq = bam1_seq(p->b);
+ // 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);
qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
// write the query sequence
for (l = qbeg; l < qend; ++l)
query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
- // do alignment; this takes most of computing time for indel calling
- if (0) {
- uint8_t *qq = calloc(qend - qbeg, 1);
- for (l = 0; l < qend - qbeg; ++l) qq[l] = 23;
+ { // do realignment; this is the bottleneck
+ const uint8_t *qual = bam1_qual(p->b), *bq;
+ uint8_t *qq;
+ qq = calloc(qend - qbeg, 1);
+ bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+ if (bq) ++bq; // skip type
+ for (l = qbeg; l < qend; ++l) {
+ qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
+ if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
+ if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
+ }
sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, qq, &kpa_par_alt, 0, 0);
- score[K*n_types + t] = sc;
- } else {
- sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, &ap);
- score[K*n_types + t] = -sc;
+ (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
+ l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
+ if (l > 255) l = 255;
+ score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l;
+ if (sc > 5) {
+ sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+ (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
+ l = (int)(100. * sc / (qend - qbeg) + .499);
+ if (l > 255) l = 255;
+ score2[K*n_types + t] = sc<<8 | l;
+ }
+ free(qq);
}
/*
for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
for (s = K = 0; s < n; ++s) {
for (i = 0; i < n_plp[s]; ++i, ++K) {
bam_pileup1_t *p = plp[s] + i;
- int *sct = &score[K*n_types], indelQ, seqQ;
+ int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
for (t = 1; t < n_types; ++t) // insertion sort
for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
* compromise for multi-allelic indels.
*/
if ((sc[0]&0x3f) == ref_type) {
- indelQ = (sc[1]>>6) - (sc[0]>>6);
+ indelQ1 = (sc[1]>>14) - (sc[0]>>14);
seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
} else {
for (t = 0; t < n_types; ++t) // look for the reference type
if ((sc[t]&0x3f) == ref_type) break;
- indelQ = (sc[t]>>6) - (sc[0]>>6);
+ indelQ1 = (sc[t]>>14) - (sc[0]>>14);
seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
}
- if (sc[0]>>6 > MAX_SCORE) indelQ = 0; // too many mismatches; something bad possibly happened
+ tmp = sc[0]>>6 & 0xff;
+ indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ
+ sct = &score2[K*n_types];
+ for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+ for (t = 1; t < n_types; ++t) // insertion sort
+ for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+ tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+ if ((sc[0]&0x3f) == ref_type) {
+ indelQ2 = (sc[1]>>14) - (sc[0]>>14);
+ } else {
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sc[t]&0x3f) == ref_type) break;
+ indelQ2 = (sc[t]>>14) - (sc[0]>>14);
+ }
+ tmp = sc[0]>>6 & 0xff;
+ 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;
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);
}
}
}
- free(score);
+ free(score1); free(score2);
// free
free(types); free(inscns);
return n_alt > 0? 0 : -1;
}
+
+#define END_SKIP 4 // must be larger than B2B_MAX_MNP
+#define MIN_MNP_FLANK_BAQ 20
+
+// the following routine is modified from bcf_call_gap_prep()
+int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref)
+{
+ extern void ks_introsort_uint32_t(int, uint32_t*);
+ int i, s, j, k, t, n_types, *types, max_rd_len, left, right, *score1;
+ int N, K, ref_seq, ref_type, n_alt;
+ char *ref2, *query;
+ uint8_t *_seqQ;
+ if (ref == 0 || bca == 0) return -1;
+ if (pos < bca->last_mnp_pos + B2B_MNP_WIN) return -2; // to avoid calling a TNP multiple times
+ if (pos < END_SKIP || ref[pos] == 0 || ref[pos+1] == 0) return -2; // end of the reference
+ { // determine if there is an MNP
+ int r[2];
+ uint8_t *tt;
+ r[0] = bam_nt16_table[(int)ref[pos]];
+ r[1] = bam_nt16_table[(int)ref[pos+1]];
+ for (s = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ int left, rght;
+ if (p->qpos < END_SKIP || p->qpos >= p->b->core.l_qseq - END_SKIP) continue;
+ tt = bam1_seq(p->b);
+ if (bam1_seqi(tt, p->qpos) == r[0] || bam1_seqi(tt, p->qpos+1) == r[1]) continue; // no MNP
+ tt = bam1_qual(p->b);
+ for (left = 0, k = p->qpos - END_SKIP; k <= p->qpos; ++k)
+ left = left > tt[k]? left : tt[k];
+ for (rght = 0, k = p->qpos; k < p->b->core.l_qseq - END_SKIP; ++k)
+ rght = rght > tt[k]? left : tt[k];
+ if (left >= MIN_MNP_FLANK_BAQ && rght >= MIN_MNP_FLANK_BAQ) break; // bracketed by good bases
+ }
+ if (i != n_plp[s]) break;
+ }
+ if (s == n) return -1; // there is no MNP at this position.
+ }
+ for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
+ { // construct the MNP consensus
+ uint8_t *tt;
+ uint32_t *aux, x, *cnt;
+ int m;
+ m = max_rd_len = 0;
+ aux = calloc(N + 1, 4);
+ for (i = 0, x = 0; i < B2B_MAX_MNP; ++i)
+ x |= bam_nt16_nt4_table[bam_nt16_table[(int)ref[pos+i]]] << 2*i;
+ ref_seq = aux[m++] = x;
+ bca->indelreg = 0;
+ for (s = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ int stop;
+ j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
+ if (j > max_rd_len) max_rd_len = j;
+ if (p->qpos < END_SKIP || p->qpos >= p->b->core.l_qseq - END_SKIP) continue;
+ tt = bam1_seq(p->b);
+ for (k = j = stop = 0, x = 0; k < B2B_MAX_MNP; ++k) {
+ int c = bam_nt16_nt4_table[bam1_seqi(tt, p->qpos + k)];
+ if (c > 3) break;
+ if (c != (ref_seq>>k*2&3) && !stop) ++j;
+ else stop = 1;
+ x |= c << 2*k;
+ }
+// fprintf(stderr, "* %d, %d\n", x, j);
+ if (k == B2B_MAX_MNP && j >= 2) aux[m++] = x;
+ }
+ }
+ ks_introsort(uint32_t, m, aux);
+ // squeeze out indentical types
+ for (i = 1, n_types = 1; i < m; ++i)
+ if (aux[i] != aux[i-1]) ++n_types;
+ if (n_types == 1) { // no indels
+ free(aux); return -1;
+ }
+ // count reads for each type
+ cnt = alloca(n_types * 4);
+ cnt[0] = 1<<8 | aux[0];
+ for (i = 1, t = 0; i < m; ++i) {
+ if (aux[i] != aux[i-1]) {
+ ++t;
+ cnt[t] = 1<<8 | aux[i];
+ } else cnt[t] += 1<<8;
+ }
+ free(aux);
+ // collect types
+ ks_introsort(uint32_t, n_types, cnt);
+ for (t = 0; t < n_types; ++t)
+ if ((cnt[t]&0xff) == ref_seq) break;
+ if (t == n_types - 1) --t; // we get at least two types
+ types = (int*)calloc(n_types, sizeof(int));
+ for (i = 0; t < n_types; ++i, ++t) types[i] = cnt[t]&0xff;
+ n_types = i;
+ // calculate MNP length
+ for (i = B2B_MAX_MNP - 1, k = 0; i >= 0; --i) {
+ int c = types[0] >> 2*i & 3;
+ for (t = 1; t < n_types; ++t)
+ if ((types[t] >> 2*i & 3) != c) break;
+ if (t == n_types) ++k;
+ else break;
+ }
+ bca->indelreg = B2B_MAX_MNP - k;
+ x = (1<<2*bca->indelreg) - 1;
+ for (t = 0; t < n_types; ++t) types[t] &= x;
+ ref_seq &= x;
+ for (t = 0; t < n_types; ++t)
+ if (types[t] == ref_seq) break;
+ ref_type = t;
+// fprintf(stderr, "%d, %d, [%x,%x] %d\n", pos, n_types, types[0], types[1], bca->indelreg);
+ }
+ { // calculate left and right boundary
+ left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
+ right = pos + INDEL_WINDOW_SIZE;
+ // in case the alignments stand out the reference
+ for (i = pos; i < right; ++i)
+ if (ref[i] == 0) break;
+ right = i;
+ }
+ { // find the highest base quality
+ _seqQ = calloc(N, 1);
+ for (s = K = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i, ++K) {
+ bam_pileup1_t *p = plp[s] + i;
+ uint8_t *qq, *bq;
+ int max = 0;
+ qq = bam1_qual(p->b);
+ bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+ if (bq) ++bq;
+ for (j = p->qpos; j < p->b->core.l_qseq && j < p->qpos + bca->indelreg; ++j) {
+ int q = bq? qq[j] + (bq[j] - 64) : qq[j];
+ max = max > q? max : q;
+ }
+ _seqQ[K] = max;
+ }
+ }
+ }
+ // compute the likelihood given each type of indel for each read
+ ref2 = calloc(right - left + 2, 1);
+ query = calloc(right - left + max_rd_len + 2, 1);
+ score1 = calloc(N * n_types, sizeof(int));
+ for (t = 0; t < n_types; ++t) {
+ int l;
+ kpa_par_t apf1 = { 1e-4, 1e-2, 10 };
+ apf1.bw = abs(types[t]) + 3;
+ // write ref2
+ for (k = 0, j = left; j < pos; ++j)
+ ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
+ for (i = 0; i < bca->indelreg; ++i, ++j)
+ ref2[k++] = types[t]>>2*i&3;
+ 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
+ for (s = K = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i, ++K) {
+ bam_pileup1_t *p = plp[s] + i;
+ int qbeg, qend, tbeg, tend, sc;
+ uint8_t *seq = bam1_seq(p->b);
+ // determine the start and end of sequences for alignment
+ qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
+ qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
+ // write the query sequence
+ for (l = qbeg; l < qend; ++l)
+ query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
+ { // do realignment; this is the bottleneck
+ const uint8_t *qual = bam1_qual(p->b), *bq;
+ uint8_t *qq;
+ qq = calloc(qend - qbeg, 1);
+ bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+ if (bq) ++bq; // skip type
+ for (l = qbeg; l < qend; ++l) {
+ qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
+ if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
+ if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
+ }
+ sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg,
+ (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
+ l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
+ if (l > 255) l = 255;
+ score1[K*n_types + t] = sc<<8 | l;
+ free(qq);
+ }
+/*
+ for (l = 0; l < tend - tbeg; ++l)
+ fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+ fputc('\n', stderr);
+ for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
+ fputc('\n', stderr);
+ fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
+*/
+ }
+ }
+ }
+ free(ref2); free(query);
+ { // compute indelQ
+ int *sc, tmp, *sumq;
+ sc = alloca(n_types * sizeof(int));
+ sumq = alloca(n_types * sizeof(int));
+ memset(sumq, 0, sizeof(int) * n_types);
+ for (s = K = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i, ++K) {
+ bam_pileup1_t *p = plp[s] + i;
+ int *sct = &score1[K*n_types], seqQ, indelQ;
+ for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+ for (t = 1; t < n_types; ++t) // insertion sort
+ for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+ tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+ if ((sc[0]&0x3f) == ref_type) {
+ indelQ = (sc[1]>>14) - (sc[0]>>14);
+ } else {
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sc[t]&0x3f) == ref_type) break;
+ indelQ = (sc[t]>>14) - (sc[0]>>14);
+ }
+ seqQ = _seqQ[K];
+ tmp = sc[0]>>6 & 0xff;
+ indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499); // reduce indelQ
+ p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
+ sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
+ }
+ }
+ // determine bca->indel_types[] and bca->inscns
+ for (t = 0; t < n_types; ++t)
+ sumq[t] = sumq[t]<<6 | t;
+ for (t = 1; t < n_types; ++t) // insertion sort
+ for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
+ tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
+ for (t = 0; t < n_types; ++t) // look for the reference type
+ if ((sumq[t]&0x3f) == ref_type) break;
+ if (t) { // then move the reference type to the first
+ tmp = sumq[t];
+ for (; t > 0; --t) sumq[t] = sumq[t-1];
+ sumq[0] = tmp;
+ }
+ for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
+ for (t = 0; t < 4 && t < n_types; ++t)
+ bca->indel_types[t] = types[sumq[t]&0x3f];
+ // update p->aux
+ for (s = n_alt = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ int x = types[p->aux>>16&0x3f];
+ for (j = 0; j < 4; ++j)
+ if (x == bca->indel_types[j]) break;
+ p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
+ if ((p->aux>>16&0x3f) > 0) ++n_alt;
+// fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d q=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, bca->indel_types[p->aux>>16&63], p->aux&0xff, p->aux>>8&0xff);
+ }
+ }
+ }
+ free(score1);
+ // free
+ free(types); free(_seqQ);
+ return n_alt > 0? 0 : -1;
+}
projects / samtools.git / blobdiff