X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=25e2a86a72958ff19aa41e88b6b003816678029c;hb=599bea10bc3487a0cbdf505e792a21a13fee2b11;hp=7359cc8855cf56d8e4c3255c23a52726401f72b7;hpb=0bb4884ffb1f4c9485efee763dd63b575f2c1381;p=samtools.git

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 7359cc8..25e2a86 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -1,14 +1,12 @@
 #include <assert.h>
+#include <ctype.h>
 #include "bam.h"
 #include "bam2bcf.h"
 #include "ksort.h"
 #include "kaln.h"
 
-#define INDEL_DEBUG
-
 #define MINUS_CONST 0x10000000
 #define INDEL_WINDOW_SIZE 50
-#define INDEL_BAD_SCORE 10000
 
 static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
 {
@@ -37,15 +35,29 @@ static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos,
 	*_tpos = x;
 	return last_y;
 }
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
 // l is the relative gap length and l_run is the length of the homopolymer on the reference
 static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
 {
 	int q, qh;
 	q = bca->openQ + bca->extQ * (abs(l) - 1);
-	qh = l_run >= 3? (int)(bca->tandemQ * (double)l / l_run + .499) : 1000;
+	qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
 	return q < qh? q : qh;
 }
 
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+	int i, j, max = 0, max_i = pos, score = 0;
+	l = abs(l);
+	for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+		if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+		else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+		if (score < 0) break;
+		if (max < score) max = score, max_i = i;
+	}
+	return max_i - pos;
+}
+
 int bcf_call_gap_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*);
@@ -53,7 +65,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	char *inscns = 0, *ref2, *query;
 	if (ref == 0 || bca == 0) return -1;
 	// determine if there is a gap
-	for (s = 0; s < n; ++s) {
+	for (s = N = 0; s < n; ++s) {
+		N += n_plp[s]; // N is the total number of reads
 		for (i = 0; i < n_plp[s]; ++i)
 			if (plp[s][i].indel != 0) break;
 		if (i < n_plp[s]) break;
@@ -62,11 +75,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	{ // find out how many types of indels are present
 		int m;
 		uint32_t *aux;
-		aux = calloc(n + 1, 4);
+		aux = calloc(N + 1, 4);
 		m = max_rd_len = 0;
 		aux[m++] = MINUS_CONST; // zero indel is always a type
-		for (s = N = 0; s < n; ++s) {
-			N += n_plp[s]; // N is the total number of reads
+		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)
@@ -151,10 +163,17 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 	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));
+	bca->indelreg = 0;
 	for (t = 0; t < n_types; ++t) {
-		int l;
+		int l, ir;
 		ka_param2_t ap = ka_param2_qual;
 		ap.band_width = 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]);
+		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]]];
@@ -178,30 +197,29 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				// 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);
-				assert(tbeg >= left);
+				if (types[t] < 0) {
+					int l = -types[t];
+					tbeg = tbeg - l > left?  tbeg - l : left;
+				}
 				// 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
-#ifdef INDEL_DEBUG
-				for (sc = 0; sc < tend - tbeg + types[t]; ++sc)
-					fputc("ACGTN"[(int)ref2[tbeg-left+sc]], stderr);
-				fputc('\n', stderr);
-				for (sc = 0; sc < qend - qbeg; ++sc) fputc("ACGTN"[(int)query[qbeg + sc]], stderr);
-				fputc('\n', stderr);				
-#endif
 				sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
 									 (uint8_t*)query + qbeg, qend - qbeg, &ap);
-#ifdef INDEL_DEBUG
-				fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
-#endif
 				score[K*n_types + t] = -sc;
+/*
+				for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+					fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+				fputc('\n', stderr);
+				for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[qbeg + l]], stderr);
+				fputc('\n', stderr);
+				fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
+*/
 			}
 		}
 	}
 	free(ref2); free(query);
-	{ // choose the top 4 indel types; reference must be included
-	}
 	{ // compute indelQ
 		int *sc, tmp, *sumq;
 		sc   = alloca(n_types * sizeof(int));
@@ -231,13 +249,14 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 					tmp = est_seqQ(bca, types[sc[0]&0x3f], l_run);
 				}
 				if (indelQ > tmp) indelQ = tmp;
-				if (indelQ > p->b->core.qual) indelQ = p->b->core.qual;
-				if (indelQ > bca->capQ) indelQ = bca->capQ;
 				p->aux = (sc[0]&0x3f)<<8 | indelQ;
 				sumq[sc[0]&0x3f] += indelQ;
+//				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);
 			}
 		}
-		// determine bca->indel_types[]
+		// determine bca->indel_types[] and bca->inscns
+		bca->maxins = max_ins;
+		bca->inscns = realloc(bca->inscns, bca->maxins * 4);
 		for (t = 0; t < n_types; ++t)
 			sumq[t] = sumq[t]<<6 | t;
 		for (t = 1; t < n_types; ++t) // insertion sort
@@ -251,10 +270,22 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 			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)
+		for (t = 0; t < 4 && t < n_types; ++t) {
 			bca->indel_types[t] = types[sumq[t]&0x3f];
+			memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+		}
+		// update p->aux
+		for (s = K = 0; s < n; ++s) {
+			for (i = 0; i < n_plp[s]; ++i, ++K) {
+				bam_pileup1_t *p = plp[s] + i;
+				int x = types[p->aux>>8&0x3f];
+				for (j = 0; j < 4; ++j)
+					if (x == bca->indel_types[j]) break;
+				p->aux = j<<8 | (j == 4? 0 : (p->aux&0xff));
+//				fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>8&63, p->aux&0xff);
+			}
+		}		
 	}
-	// FIXME: to set the inserted sequence
 	free(score);
 	// free
 	free(types); free(inscns);