From f9a70d72dee269611204c6ba9dd78034bba45620 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 27 Nov 2023 19:56:06 -0800
Subject: [PATCH] Verify that VCF 4.3 files with a "v4.4" header can be parsed.
 Fixes #1289

---
 .../broad/igv/variant/vcf/VCFVariantTest.java | 20 +++++++++++++++++++
 test/data/vcf/fake_v4.vcf                     | 15 ++++++++++++++
 2 files changed, 35 insertions(+)
 create mode 100644 test/data/vcf/fake_v4.vcf

diff --git a/src/test/java/org/broad/igv/variant/vcf/VCFVariantTest.java b/src/test/java/org/broad/igv/variant/vcf/VCFVariantTest.java
index 4fd7f359bd..44da2f550b 100644
--- a/src/test/java/org/broad/igv/variant/vcf/VCFVariantTest.java
+++ b/src/test/java/org/broad/igv/variant/vcf/VCFVariantTest.java
@@ -95,4 +95,24 @@ private VCFVariant tstStart(String chr, int fileFeatStart, VariantContext.Type v
         assertEquals(expFeatStart, variant.getStart());
         return variant;
     }
+
+    /**
+     * Just verifies IGV will read a file marked vcf4.4 in the header, actual format is 4.1.
+     *
+     * @return
+     * @throws Exception
+     */
+    @Test
+    public void tstFakeV4() throws Exception{
+
+        System.setProperty("samjdk.optimistic_vcf_4_4", "true");
+
+        String filePath = TestUtils.DATA_DIR + "vcf/fake_v4.vcf";
+        TestUtils.createIndex(filePath);
+        TribbleFeatureSource src = TribbleFeatureSource.getFeatureSource(new ResourceLocator(filePath), genome);
+
+        VCFVariant variant = (VCFVariant) (src.getFeatures("chr20", 10499352 - 5, 10499352 + 5)).next();
+        assertEquals(VariantContext.Type.INDEL.toString(), variant.getType());
+        assertEquals(10499351, variant.getStart());
+    }
 }
diff --git a/test/data/vcf/fake_v4.vcf b/test/data/vcf/fake_v4.vcf
new file mode 100644
index 0000000000..d6db4304d5
--- /dev/null
+++ b/test/data/vcf/fake_v4.vcf
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.4
+##contig=<ID=20,length=63025520,assembly=b37>
+##reference=human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+20	10499005	.	T	C	6913.77	.	AC=2;AF=1.00;AN=2;DP=43;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=175.86;MQ0=0;QD=28.20	GT:AD:GQ:PL	1/1:0,38:99:6942,147,0
+20	10499052	.	T	TTTCTTTCC	481.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.060;ClippingRankSum=-0.555;DP=28;FS=4.269;MLEAC=1;MLEAF=0.500;MQ=151.80;MQ0=0;MQRankSum=1.109;QD=2.15;ReadPosRankSum=0.079	GT:AD:GQ:PL	0/1:13,7:99:519,0,723
+20	10499073	.	CG	TA	.	.	AC=2;AF=1.00;AN=2;DP=43;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=175.86;MQ0=0;QD=28.20	GT:AD:GQ:PL	1/1:0,38:99:6942,147,0
+20	10499099	.	CTTCCTTCCTTCCTTTCCTTTCTTTTCCT	C	481.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.896;ClippingRankSum=-1.001;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=126.32;MQ0=0;MQRankSum=1.001;QD=0.78;ReadPosRankSum=-0.065	GT:AD:GQ:PL	0/1:12,5:99:519,0,691
+20	10499111	.	CTTTCCTTTCTTTTCCT	C	589.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;ClippingRankSum=1.395;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=123.59;MQ0=0;MQRankSum=-0.667;QD=1.76;ReadPosRankSum=-0.934	GT:AD:GQ:PL	0/1:4,12:99:627,0,519
+20	10499180	.	TCC	T	481.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;ClippingRankSum=0.358;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=131.07;MQ0=0;MQRankSum=1.231;QD=18.53;ReadPosRankSum=0.358	GT:AD:GQ:PL	0/1:3,2:99:519,0,722
+20	10499183	.	TTCCTTCCTTCCTTC	T	481.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;ClippingRankSum=0.358;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=154.10;MQ0=0;MQRankSum=1.231;QD=2.02;ReadPosRankSum=0.000	GT:AD:GQ:PL	0/1:3,2:99:519,0,654
+20	10499188	.	TCC	T	683.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.000;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=148.61;MQ0=0;MQRankSum=-1.026;QD=26.30;ReadPosRankSum=0.000	GT:AD:GQ:PL	0/1:2,2:99:721,0,519
+20	10499191	.	TTCCTTC	T	584.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.000;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=158.63;MQ0=0;MQRankSum=-1.026;QD=6.09;ReadPosRankSum=0.000	GT:AD:GQ:PL	0/1:2,2:99:622,0,519
+20	10499291	.	TTCCTTC	A	584.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.000;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=158.63;MQ0=0;MQRankSum=-1.026;QD=6.09;ReadPosRankSum=0.000	GT:AD:GQ:PL	0/1:2,2:99:622,0,519
+20	10499352	.	T	ATTCTTTCC	481.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.060;ClippingRankSum=-0.555;DP=28;FS=4.269;MLEAC=1;MLEAF=0.500;MQ=151.80;MQ0=0;MQRankSum=1.109;QD=2.15;ReadPosRankSum=0.079	GT:AD:GQ:PL	0/1:13,7:99:519,0,723
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