minor updates

inc/vcf/validator_detail_v44.hpp

@@ -17,7 +17,7 @@
  */
 
 
-#line 263 "src/vcf/vcf_v44.ragel"
+#line 268 "src/vcf/vcf_v44.ragel"
 
 
 namespace
@@ -185,7 +185,7 @@ static const int vcf_v44_en_meta_section_skip = 667;
 static const int vcf_v44_en_body_section_skip = 668;
 
 
-#line 269 "src/vcf/vcf_v44.ragel"
+#line 274 "src/vcf/vcf_v44.ragel"
 
 }
 
@@ -204,7 +204,7 @@ namespace ebi
 	cs = vcf_v44_start;
 	}
 
-#line 283 "src/vcf/vcf_v44.ragel"
+#line 288 "src/vcf/vcf_v44.ragel"
 
     }
 
@@ -8133,11 +8133,11 @@ case 681:
     }
 	break;
 	case 75:
-#line 261 "src/vcf/vcf_v44.ragel"
+#line 266 "src/vcf/vcf_v44.ragel"
 	{ {cs = 28;goto _again;} }
 	break;
 	case 76:
-#line 262 "src/vcf/vcf_v44.ragel"
+#line 267 "src/vcf/vcf_v44.ragel"
 	{ {cs = 673;goto _again;} }
 	break;
 #line 8144 "inc/vcf/validator_detail_v44.hpp"
@@ -8632,7 +8632,7 @@ goto _again;}
 	_out: {}
 	}
 
-#line 291 "src/vcf/vcf_v44.ragel"
+#line 296 "src/vcf/vcf_v44.ragel"
 
     }
 

src/vcf/record.cpp

@@ -1003,8 +1003,8 @@ namespace ebi
                     + " is not one of [A, R, G, ., <non-negative number>]"));
         }
         if(!values.empty()) {
-            if (values.front() == MISSING_VALUE) { return; } // No need to check missing data
-        } //TODO, if the 1st one is . then check stops; svclaim=.,DJ worked!
+            if (values.front() == MISSING_VALUE && values.size() == 1) { return; } // No need to check missing data
+        }
 
         bool number_matches = true;
         if (expected_cardinality > 0) {

src/vcf/vcf_v44.ragel

@@ -222,7 +222,12 @@
     ## Accepting non-alphanumeric characters is an addition in v4.3, but widely used in already existing files
     format_value    = ( (alpha | '_') (alnum | '_' | '.' | '%')* ) >token_begin $token_middle %token_end ;
     record_format   = format_value (':' format_value)* ;
-
+
+    ## NOTE: The genotype definition shows the format in which it is expected but won't get enforced from ragel
+    ## as sample_values is a super set of genotype and other chars. Invalid genotypes successfully passes through
+    ## ragel checks. The validation of genotype takes place in c++ code and not in ragel space.
+    ## Same is applicable for older version as well.
+
     ## In a sample, if a genotype is present it must be the first field
     record_sample   = (
                         genotype $eof(no_newline_at_eof_error) $err(genotype_error) (':' sample_values)? |