X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=8b80e3fc55d79751f0866814d87ce52cba39b858;hb=4c8c9dfc1e3b3b066a62a703fd3ba04db6ad5a45;hp=819c1e7b1371296b7da5536939fab691f53c1722;hpb=624c76e0c2b7f98b0fdf734345a61e3019e68fd3;p=samtools.git

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 819c1e7..8b80e3f 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -408,3 +408,258 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	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;
+}