bugfix: missing values are not filled sometimes

samtools · Jun 20, 2012 · 9ea927a · 9ea927a
1 parent ffc8d65
commit 9ea927a
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Showing 2 changed files with 19 additions and 1 deletion.
diff --git a/htslib/vcf.c b/htslib/vcf.c
@@ -707,6 +707,24 @@ int vcf_parse1(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
 					for (; l != z->size>>2; ++l) *(int32_t*)(x+l) = bcf_missing_float;
 				} else abort();
 				if (*t == 0) {
+					for (++j; j < v->n_fmt; ++j) { // fill missing values
+						z = &fmt[j];
+						if ((z->y>>4&0xf) == BCF_HT_STR) {
+							if (z->is_gt) {
+								int32_t *x = (int32_t*)(z->buf + z->size * m);
+								for (l = 0; l != z->size>>2; ++l) x[l] = INT32_MIN;
+							} else {
+								char *x = (char*)z->buf + z->size * m;
+								for (l = 0; l != z->size; ++l) x[l] = 0;
+							}
+						} else if ((z->y>>4&0xf) == BCF_HT_INT) {
+							int32_t *x = (int32_t*)(z->buf + z->size * m);
+							for (l = 0; l != z->size>>2; ++l) x[l] = INT32_MIN;
+						} else if ((z->y>>4&0xf) == BCF_HT_REAL) {
+							float *x = (float*)(z->buf + z->size * m);
+							for (l = 0; l != z->size>>2; ++l) *(int32_t*)(x+l) = bcf_missing_float;
+						}
+					}
 					if (t == end) break;
 					++m, j = 0;
 				} else if (*t == ':') ++j;

diff --git a/test/ex2.vcf b/test/ex2.vcf
@@ -19,5 +19,5 @@
 20	14370	rs6054257	G	A	29.1	.	NS=3;DP=14;AF=0.5;HOMSEQ;DB	GT:GQ:DP:HQ:CNL	0|0:48:1:25,30:10,20	1|0:48:8:49,51:.	./.:43:5:.,.:1
 20	17330	.	T	A	.	q10;s50	NS=3;DP=11;AF=0.017;H2	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:4,5
 20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:10,20
-20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:0,3
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	./.
 20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3