X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam2bcf_indel.c;fp=bam2bcf_indel.c;h=4f747b156f439bf5d6e516cea3856bf5054e831c;hp=954e43e8f85a404704b48fb5a6191c247baaaf6d;hb=ea1bf85308be7146d11a0153391d99fcfb3f83ad;hpb=4ec3d44869c8aac4db819d48a230b00e05691a57

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 954e43e..4f747b1 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -412,14 +412,11 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 #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;
+	int i, s, j, k, t, n_types, *types;
+	int N, ref_seq, ref_type;
 	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
@@ -450,8 +447,7 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	{ // construct the MNP consensus
 		uint8_t *tt;
 		uint32_t *aux, x, *cnt;
-		int m;
-		m = max_rd_len = 0;
+		int m = 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;
@@ -461,8 +457,6 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 			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) {
@@ -472,10 +466,12 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 					else stop = 1;
 					x |= c << 2*k;
 				}
-//				if (j >= 2 && k == B2B_MAX_MNP) fprintf(stderr, "* %c%c%c%c, %d\n", "ACGT"[x&3], "ACGT"[x>>2&3], "ACGT"[x>>4&3], "ACGT"[x>>6&3], j);
 				if (k == B2B_MAX_MNP && j >= 2) aux[m++] = x;
 			}
 		}
+		if (m == 0) {
+			free(aux); return -1;
+		}
 		ks_introsort(uint32_t, m, aux);
 		// squeeze out indentical types
 		for (i = 1, n_types = 1; i < m; ++i)
@@ -490,170 +486,75 @@ int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 			} else cnt[t] += 1<<8;
 		}
 		free(aux);
-		// collect types
+		// collect types; NOTE: we only collect ONE alternative type
 		ks_introsort(uint32_t, n_types, cnt);
-		if (n_types == 1 || (cnt[n_types-1]>>8) * MIN_SUPPORT_COEF < N) // no MNPs or too few supporting reads
+		if ((cnt[n_types-1]>>8) * MIN_SUPPORT_COEF < N) // no MNPs or too few supporting reads
 			return -1;
 		types = (int*)calloc(2, sizeof(int));
-		types[0] = ref_seq; types[1] = cnt[n_types-1]&0xff;
+		bca->indel_types[0] = types[0] = ref_seq;
+		bca->indel_types[1] = types[1] = cnt[n_types-1]&0xff;
+		bca->indel_types[2] = bca->indel_types[3] = B2B_INDEL_NULL;
 		ref_type = 0; n_types = 2;
 		// calculate MNP length
-		for (i = B2B_MAX_MNP - 1, k = 0; i >= 0; --i) {
+		for (i = 0; i < B2B_MAX_MNP; ++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;
+			if (t == n_types) break;
 		}
-		bca->indelreg = B2B_MAX_MNP - k;
+		bca->indelreg = i;
+		if (bca->indelreg < 2) return -1; // should not happen in principle
 		x = (1<<2*bca->indelreg) - 1;
 		for (t = 0; t < n_types; ++t) types[t] &= x;
 		ref_seq &= x;
-//		x = types[1]; fprintf(stderr, "%d, %d, %d, %c%c%c%c\n", pos, n_types, bca->indelreg, "ACGT"[x&3], "ACGT"[x>>2&3], "ACGT"[x>>4&3], "ACGT"[x>>6&3]);
 	}
-	{ // 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) {
+	{ // calling
+		for (s = 0; s < n; ++s) {
+			for (i = 0; i < n_plp[s]; ++i) {
 				bam_pileup1_t *p = plp[s] + i;
-				uint8_t *qq, *bq;
-				int max = 0;
+				uint8_t *qq, *bq, *seq = bam1_seq(p->b);
+				uint32_t x, *cigar = bam1_cigar(p->b);
+				int y, skip = 0, baseQ = 0, baq = 0;
+				// try to get the original base quality
 				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) {
+				// get the max original base quality
+				for (j = p->qpos, x = 0; 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;
+					int c = bam_nt16_nt4_table[bam1_seqi(seq, j)];
+					baseQ = baseQ > q? baseQ : q;
+					if (c > 3) skip = 1;
+					x |= c << 2 * (j - p->qpos);
 				}
-				_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;
+				for (t = 0; t < n_types; ++t)
+					if (types[t] == x) break;
+				if (t == n_types) skip = 1;
+				else { // reapply BAQ
+					for (k = y = 0; k < p->b->core.n_cigar; ++k) {
+						int op = cigar[k]&0xf;
+						int len = cigar[k]>>4;
+						if (op == BAM_CMATCH) {
+							if (p->qpos >= y && p->qpos + bca->indelreg <= y + len) {
+								int left, rght;
+								for (j = y, left = 0; j <= p->qpos; ++j)
+									left = left > qq[j]? left : qq[j];
+								for (j = p->qpos + bca->indelreg - 1, rght = 0; j < y + len; ++j)
+									rght = rght > qq[j]? rght : qq[j];
+								baq = left < rght? left : rght;
+								break;
+							}
+							y += len;
+						} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += len;
 					}
-					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
-				if (indelQ > seqQ) indelQ = seqQ; // this is different from indel calling!
-				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 skip=%d reg=%d call=%d baseQ=%d baq=%d\n", pos+1, s, i, bam1_qname(p->b), skip, bca->indelreg, t, baseQ, baq);
+				baseQ = baseQ < baq? baseQ : baq;
+				p->aux = skip? 0 : (t<<16|baseQ<<8|baseQ);
 			}
 		}
-		// 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;
+	free(types);
+	return 0;
 }