Merge pull request #229 from PolinaBevad/fix_issue_225_vcf_merge

Fixed issue 225 (vcf merge fail)

src/main/java/com/astrazeneca/vardict/modules/ToVarsBuilder.java

@@ -763,7 +763,7 @@ else if (deletionLength < instance().conf.SVMINLEN) {
                         startPosition++;
                     }
 
-                    if (varallele.equals("<DEL>") && refallele.length() > 1) {
+                    if (varallele.equals("<DEL>") && refallele.length() >= 1) {
                         refallele = ref.containsKey(startPosition) ? ref.get(startPosition).toString() : "";
                         if (refCoverage.containsKey(startPosition - 1)) {
                             totalPosCoverage = refCoverage.get(startPosition - 1);

testdata/integrationtestcases/Simple;GRCh37.fa;NA24385.REF.SVDEL.bam;chr1;9011935-9017839;-f 0.001.txt

@@ -0,0 +1,24 @@
+Simple,GRCh37.fa,NA24385.REF.SVDEL.bam,chr1,9011935,9017839,-f 0.001
+NA24385.REF.SVDEL	testbed	1	9012379	9012379	A	T	61	2	29	30	0	2	A/T	0.0328	2;0	38.0	0	42.0	0	60.0	4.000	0.0357	0	0	2.000	2	1.5	2	56	CTAATTTTTGTATTTTTTGT	GAGATGGGGTTTCAGCATGT	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9012433	9012433	T	A	61	2	34	25	1	1	T/A	0.0328	2;2	6.0	0	39.5	1	60.0	4.000	0.0345	0	0	1.000	1	2.5	2	58	CTCGAACTCCTGACCTCAAG	GATCCGCCCACCTTGGCCTC	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9012476	9012476	A	G	87	33	29	22	23	10	A/G	0.3793	2;2	22.5	1	39.7	1	57.9	66.000	0.3882	0.0345	0	1.000	1	1.7	33	85	AAAGTGTTGAGATTATATGC	TAAGCCACCGTGCCCAGCCT	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9012476	9012478	ATA	GT	87	2	29	22	2	0	ATA/-1GT	0.0230	2;0	25.0	1	42.0	1	60.0	4.000	0.0235	0.0115	0	1.000	1	1.5	2	85	AAAGTGTTGAGATTATATGC	AGCCACCGTGCCCAGCCTGA	1:9011936-9017839	Complex	0	0
+NA24385.REF.SVDEL	testbed	1	9012239	9012239	A	C	49	2	25	22	0	2	A/C	0.0408	2;0	9.0	1	26.2	1	58.5	4.000	0.0455	0.0204	0	2.000	1	2.0	2	44	GGAGTCTCACTCTGTCACCC	GGCTGGAATGCAGTGGCATG	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9011230	9012280	G	<DEL>	61	3	0	0	3	0	-1050AC/-1050A	0.0492	0;0	32.0	1	38.9	1	60.0	6.000	1.0000	0.0492	0	0	0	1.0	3	3	GGTTGCAGTGAGCCAAGATC	TGCCTCCTAGGGTCAAGCAA	1:9011936-9017839	DEL	0	3-0-0
+NA24385.REF.SVDEL	testbed	1	9017394	9017395	CT	C	41	2	19	20	2	0	T/-1	0.0488	2;0	29.0	0	42.0	0	60.0	4.000	0.0488	0	3	4.000	1	0	2	41	TCCTTTGAACCCCATAGTCA	TTTCTTTTTATTTATTTATT	1:9011936-9017839	Deletion	0	0
+NA24385.REF.SVDEL	testbed	1	9012610	9012610	G	GA	97	3	44	48	2	1	G/+1	0.0309	2;2	31.3	1	33.7	1	60.0	2.000	0.0222	0	7	8.000	1	0.3	2	90	CAGGAATTCTACTGAAGGGG	AAAAAAAGCTAATCTACAAA	1:9011936-9017839	Insertion	0	0
+NA24385.REF.SVDEL	testbed	1	9012625	9012625	T	A	83	2	38	43	1	1	T/A	0.0241	2;2	35.0	1	34.5	1	60.0	4.000	0.0241	0	0	1.000	1	2.0	2	83	AGGGGGAAAAAAAGCTAATC	ACAAACTTTGAATCTAATGA	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9012705	9012705	A	AT	76	2	36	37	2	0	A/+1	0.0263	2;0	51.0	0	42.0	0	60.0	4.000	0.0290	0	5	6.000	1	2.1	2	69	GACGTATTAAAGATTTGTTA	TTTTTGGTTTTGCAAGGTTC	1:9011936-9017839	Insertion	0	0
+NA24385.REF.SVDEL	testbed	1	9012488	9012489	GC	G	88	4	48	36	2	2	C/-1	0.0455	2;2	28.5	1	38.9	1	60.0	8.000	0.0494	0.0227	2	3.000	1	1.0	4	81	TTATATGCATAAGCCACCGT	CCAGCCTGATATAAAGTATT	1:9011936-9017839	Deletion	0	0
+NA24385.REF.SVDEL	testbed	1	9017700	9017700	G	T	23	2	2	19	0	2	G/T	0.0870	2;0	5.0	0	42.0	0	48.0	4.000	0.0952	0	0	1.000	1	2.0	2	21	GTGAGCCACAGTGCCCAGCC	TCACTTTTCTTATTAAAATA	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9012605	9012605	A	AG	100	3	46	49	0	3	A/+1	0.0300	2;0	42.7	1	26.7	1	60.0	2.000	0.0215	0.0100	5	6.000	1	1.0	2	93	ACATTCAGGAATTCTACTGA	GGGGGAAAAAAAGCTAATCT	1:9011936-9017839	Insertion	0	0
+NA24385.REF.SVDEL	testbed	1	9016974	9016975	GT	G	54	2	40	11	0	2	T/-1	0.0370	2;0	28.0	0	42.0	0	60.0	4.000	0.0435	0	2	3.000	1	0	2	46	AGAGGCACTTGCCCAGCCTG	TTACTTAGTGCCTGGCCTCC	1:9011936-9017839	Deletion	0	0
+NA24385.REF.SVDEL	testbed	1	9016976	9016976	T	TTACTTAGTGCCTGGCCTCCATCCTGACCTCACCCTGTGCCCTGTGCGCAAACGCCTCTTCTCCTTTGGTGACCCTGCCCATGGCATTCTAAGCCAGTCTATGGTATTGGCTTGCCCTGGGCTCAGACAGGTGGGAGGTGAGCAGAGAAGCTACCCAGCCTGTAGGCCTGACCCCTCTGTGTTCACCTACTCTGCTCTCAGCCCCACCTTGTCTCTCCAGTGCAGATCAGCCTGCCCTCCACCATGCGCATGACAGTGGCTGACGGCACTGTATACATAGCCCAGCAGATGCACTTTCACTGGGGAGGTGCGTCCTCGGAGATCAGCGGCTCTGAGCACACCGTGGACGGGATC	63	3	38	13	3	0	T/+353	0.0476	2;0	61.0	1	41.9	1	60.0	6.000	0.0625	0.0476	70	3.000	1	0	3	48	AGGCACTTGCCCAGCCTGGT	TACTTAGTGCCTGGCCTCCA	1:9011936-9017839	Insertion	0	3-0-0
+NA24385.REF.SVDEL	testbed	1	9017003	9017005	CCT	C	56	2	35	19	1	1	C/-2	0.0357	2;2	59.5	1	42.0	0	60.0	4.000	0.0364	0	1	2.000	1	0	2	55	GTGCCTGGCCTCCATCCTGA	CACCCTGTGCCCTGTGCGCA	1:9011936-9017839	Deletion	0	0
+NA24385.REF.SVDEL	testbed	1	9012776	9012776	C	T	65	32	18	15	21	11	C/T	0.4923	2;2	40.9	1	37.6	1	58.9	9.667	0.4677	0	0	2.000	2	1.6	29	62	CCCAGGCTGGAGTGCGGTGG	GCGATCTCGGCTCACTGCAA	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9017248	9017248	A	C	47	2	15	30	2	0	A/C	0.0426	2;0	7.0	0	42.0	0	60.0	4.000	0.0465	0	0	1.000	1	1.5	2	43	ACAGTGGCTGACGGCACTGT	TACATAGCCCAGCAGATGCA	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9017322	9017322	A	G	62	3	20	39	1	2	A/G	0.0484	2;2	41.3	1	30.3	1	60.0	2.000	0.0357	0	0	1.000	1	2.3	2	56	CGGCTCTGAGCACACCGTGG	CGGGATCAGACATGTGATCG	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9011999	9011999	T	C	52	21	16	15	11	10	T/C	0.4038	2;2	35.8	1	40.8	1	57.3	42.000	0.4200	0.0192	3	2.000	1	1.4	21	50	AGCAATTCTCCTGCCTCAGC	TCCCTGGTACCTGGGACTAC	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9017122	9017123	GA	G	85	2	39	44	2	0	A/-1	0.0235	2;0	31.0	0	42.0	0	60.0	4.000	0.0253	0	1	3.000	2	0	2	79	ACAGGTGGGAGGTGAGCAGA	AGCTACCCAGCCTGTAGGCC	1:9011936-9017839	Deletion	0	0
+NA24385.REF.SVDEL	testbed	1	9013096	9013096	T	C	6	4	0	2	0	4	T/C	0.6667	0;0	35.0	1	40.8	1	60.0	8.000	0.6667	0	0	3.000	1	1.8	4	6	TGTGTTCCACCTGTTCATCT	TCCCTTCCTTCCTAAACCCT	1:9011936-9017839	SNV	0	0
+NA24385.REF.SVDEL	testbed	1	9017204	9017204	A	G	54	23	7	24	9	14	A/G	0.4259	2;2	28.9	1	39.0	1	60.0	46.000	0.4510	0	1	1.000	1	1.8	23	51	TTGTCTCTCCAGTGCAGATC	GCCTGCCCTCCACCATGCGC	1:9011936-9017839	SNV	0	0