X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=819c1e7b1371296b7da5536939fab691f53c1722;hb=30004e9139b96449fa34831af2fd8e860567a29d;hp=7f6e288014cf1e0b627f3e7f2150e6dfbef5a03d;hpb=fe9d679264cafa551db00fe309eea2858a536ee8;p=samtools.git

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 7f6e288..819c1e7 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -11,7 +11,7 @@ KHASH_SET_INIT_STR(rg)
 
 #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)
 {
@@ -112,7 +112,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 					  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;
@@ -141,7 +142,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	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;
@@ -149,8 +150,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 		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;
 			}
@@ -159,7 +165,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 		// 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));
@@ -232,12 +238,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	// 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]);
@@ -264,6 +271,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				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);
@@ -274,17 +282,30 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				// 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)
@@ -306,7 +327,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 		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)
@@ -318,15 +339,32 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				 * 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);
@@ -365,7 +403,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 			}
 		}		
 	}
-	free(score);
+	free(score1); free(score2);
 	// free
 	free(types); free(inscns);
 	return n_alt > 0? 0 : -1;