Bug fix in GT field creation when dealing with Java - reported

#161

Fixed CI golden output that if correct would have caught this bug :(

src/main/cpp/include/vcf/vcf.h

@@ -141,6 +141,13 @@ inline T get_bcf_gt_missing_value() { return static_cast<T>(bcf_gt_missing); }
 template<>
 inline std::string get_bcf_gt_missing_value<std::string>() { return ""; }
 
+//GT missing value - purely for compilation to proceed with std::string
+template<class T>
+inline T get_bcf_gt_no_call_allele_index() { return static_cast<T>(-1); }
+
+//string specialization
+template<>
+inline std::string get_bcf_gt_no_call_allele_index<std::string>() { return ""; }
 
 //for float, equality is not an adequate check
 template<>

src/main/cpp/src/genomicsdb/variant_field_handler.cc

@@ -754,7 +754,7 @@ bool VariantFieldHandler<DataType>::collect_and_extend_fields(const Variant& var
         (use_vector_end_only || (is_GT_field && !use_missing_values_only_not_vector_end))
         ? get_bcf_vector_end_value<DataType>()
         : ((is_GT_field && use_missing_values_only_not_vector_end)
-            ? get_bcf_gt_missing_value<DataType>() //why? htsjdk does not handle a record where GT is missing in 1 sample, present in another
+            ? get_bcf_gt_no_call_allele_index<DataType>()  //why? htsjdk does not handle a record where GT is missing in 1 sample, present in another. So, set GT value to no-call
             : get_bcf_missing_value<DataType>());
       ++num_elements_inserted;
       ++extended_field_vector_idx;

tests/golden_outputs/t0_haploid_triploid_1_2_3_triploid_deletion_java_vcf_produce_GT

@@ -117,9 +117,9 @@
 ##contig=<ID=NC_007605,length=171823>
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00141	HG01958	HG01530	NA12878
-1	12141	.	C	<NON_REF>	.	.	END=12144	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	0	0	0
-1	12145	.	C	<NON_REF>	.	.	END=12277	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	0/0:3:0:0:0,0,0	0	0
-1	12278	.	C	<NON_REF>	.	.	END=12295	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	0	0	0
-1	17384	.	TGG	T,TG,<NON_REF>	.	.	BaseQRankSum=1.07;ClippingRankSum=-1.067e+00;DP=9;MQ=55.72;MQ0=0;MQRankSum=0.056	GT:AD:DP:GQ:PL:SB	0	0	0	0/1/0:6,2,3,0:8:40:40,0,197,58,203,262,123,456,789,12,0,1,2,3,4,5,6,7,8,9:0,0,0,0
+1	12141	.	C	<NON_REF>	.	.	END=12144	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	.	.	.
+1	12145	.	C	<NON_REF>	.	.	END=12277	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	0/0:3:0:0:0,0,0	.	.
+1	12278	.	C	<NON_REF>	.	.	END=12295	GT:DP:GQ:MIN_DP:PL	0:2:0:0:0,0	.	.	.
+1	17384	.	TGG	T,TG,<NON_REF>	.	.	BaseQRankSum=1.07;ClippingRankSum=-1.067e+00;DP=9;MQ=55.72;MQ0=0;MQRankSum=0.056	GT:AD:DP:GQ:PL:SB	.	.	.	0/1/0:6,2,3,0:8:40:40,0,197,58,203,262,123,456,789,12,0,1,2,3,4,5,6,7,8,9:0,0,0,0
 1	17385	.	G	A,T,*,<NON_REF>	.	.	BaseQRankSum=-2.074e+00;ClippingRankSum=-1.859e+00;DP=285;MQ=31.72;MQ0=3;MQRankSum=-4.320e-01;RAW_MQ=2.50;ReadPosRankSum=5.000e-03	GT:AD:DP:GQ:PGT:PID:PL:SB	0/1/0:58,22,17,17,17:80:99:0|1:17385_G_A:504,0,9807,678,1870,2548,123,456,789,12,1870,2548,123,456,789,12,456,789,12,12,1870,2548,123,456,789,12,456,789,12,12,456,789,12,12,12:58,0,22,0	2/2:0,37,120,37,37:120:99:0|1:17385_G_T:3336,4536,7349,358,958,0,4536,7349,958,7349,4536,7349,958,7349,7349:0,0,0,0	0/1:40,36,0,0,0:76:99:.:.:1018,0,1116,1137,1224,2361,1137,1224,2361,2361,1137,1224,2361,2361,2361:9,31,13,23	0/4/0:6,0,0,3,0:8:40:.:.:40,0,6,9,0,6,9,6,9,9,203,3,8,3,8,8,456,5,5,12,0,6,9,6,9,9,3,8,8,5,6,9,9,8,9:0,0,0,0
-1	17386	.	G	*,<NON_REF>	.	.	DP=9	GT:AD:DP:GQ:PL:SB	0	0	0	0/2/0:6,3,0:8:40:40,203,456,12,0,3,5,6,8,9:0,0,0,0
+1	17386	.	G	*,<NON_REF>	.	.	DP=9	GT:AD:DP:GQ:PL:SB	.	.	.	0/2/0:6,3,0:8:40:40,203,456,12,0,3,5,6,8,9:0,0,0,0