X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf_indel.c;h=2254cf038d34d4c7f0938549b85e0c43befe62af;hb=e561d6e1a3c58df4de0e2856c2cfb9b2b68e7f11;hp=7ae6be0f18b0b7940ae840c84dfed5ff9a17f5a1;hpb=53afc90ef53f3c5cd3060377f16828363f55ed00;p=samtools.git

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 7ae6be0..2254cf0 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)
 {
@@ -37,6 +35,7 @@ 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)
 {
@@ -46,6 +45,19 @@ static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
 	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*);
@@ -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]]];
@@ -187,16 +206,16 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 					query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
 				// do alignment; this takes most of computing time for indel calling
 				sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
-									 (uint8_t*)query + qbeg, qend - qbeg, &ap);
+									 (uint8_t*)query, qend - qbeg, &ap);
 				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);
+				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 score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
-//*/
+				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);
+*/
 			}
 		}
 	}
@@ -209,7 +228,7 @@ 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;
+				int *sct = &score[K*n_types], indelQ, seqQ;
 				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)
@@ -222,23 +241,21 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
 				 */
 				if ((sc[0]&0x3f) == ref_type) {
 					indelQ = (sc[1]>>6) - (sc[0]>>6);
-					tmp = est_seqQ(bca, types[sc[1]&0x3f], l_run);
+					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);
-					tmp = est_seqQ(bca, types[sc[0]&0x3f], l_run);
+					seqQ = 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,%d\n", pos, s, i, bam1_qname(p->b),
-						types[sc[0]&0x3f], indelQ, tmp);
+				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);
 			}
 		}
-		// 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
@@ -252,10 +269,22 @@ 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>>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));
+//				fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, p->aux&0xff);
+			}
+		}		
 	}
-	// FIXME: to set the inserted sequence
 	free(score);
 	// free
 	free(types); free(inscns);