Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
VCFReaderTest	37	77	5	0.8048780680.5%	Show methods

Class VCFReaderTest

Class VCFReaderTest	Line # 37	Total Statements 77	Complexity 5	TOTAL Coverage 0.8048780680.5%
testReadVcf_plain() : void   testReadVcf_plain() : void	5656	38.038	1.01	1.0 1.0100%
writeVcfFile() : File   writeVcfFile() : File	119119	7.07	1.01	1.0 1.0100%
testQuery_indexed() : void   testQuery_indexed() : void	138138	11.011	1.01	0.0 0.00%
printNext(CloseableIterator<VariantContext>) : int   printNext(CloseableIterator<VariantContext>) : int	174174	3.03	1.01	0.0 0.00%
testQuery_plain() : void   testQuery_plain() : void	188188	18.018	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.5731707	jalview.ext.htsjdk.VCFReaderTest.testReadVcf_plainjalview.ext.htsjdk.VCFReaderTest.testReadVcf_plain	1PASS
	0.3292683	jalview.ext.htsjdk.VCFReaderTest.testQuery_plainjalview.ext.htsjdk.VCFReaderTest.testQuery_plain	1PASS

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ext.htsjdk;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26		import htsjdk.samtools.util.CloseableIterator;
27		import htsjdk.variant.variantcontext.Allele;
28		import htsjdk.variant.variantcontext.VariantContext;
29
30		import java.io.File;
31		import java.io.IOException;
32		import java.io.PrintWriter;
33		import java.util.List;
34
35		import org.testng.annotations.Test;
36
		80.5% Uncovered Elements: 16 (82) Complexity: 5 Complexity Density: 0.06
37		public class VCFReaderTest
38		{
39		private static final String[] VCF = new String[] { "##fileformat=VCFv4.2",
40		"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
41		"20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
42		"20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
43		"18\t2\t.\tACG\tA\t.\tPASS\tDP=100" }; // deletion ACG/A
44
45		// gnomAD exome variant dataset
46		private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";
47
48		// "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
49
50		/**
51		* A test to exercise some basic functionality of the htsjdk VCF reader,
52		* reading from a non-index VCF file
53		*
54		* @throws IOException
55		*/
		100% Uncovered Elements: 0 (38) Complexity: 1 Complexity Density: 0.03 1PASS
56	1	@Test(groups = "Functional")...
57		public void testReadVcf_plain() throws IOException
58		{
59	1	File f = writeVcfFile();
60	1	VCFReader reader = new VCFReader(f.getAbsolutePath());
61	1	CloseableIterator<VariantContext> variants = reader.iterator();
62
63		/*
64		* SNP C/G variant
65		*/
66	1	VariantContext vc = variants.next();
67	1	assertTrue(vc.isSNP());
68	1	Allele ref = vc.getReference();
69	1	assertEquals(ref.getBaseString(), "C");
70	1	List<Allele> alleles = vc.getAlleles();
71	1	assertEquals(alleles.size(), 2);
72	1	assertTrue(alleles.get(0).isReference());
73	1	assertEquals(alleles.get(0).getBaseString(), "C");
74	1	assertFalse(alleles.get(1).isReference());
75	1	assertEquals(alleles.get(1).getBaseString(), "G");
76
77		/*
78		* Insertion G -> GA
79		*/
80	1	vc = variants.next();
81	1	assertFalse(vc.isSNP());
82	1	assertTrue(vc.isSimpleInsertion());
83	1	ref = vc.getReference();
84	1	assertEquals(ref.getBaseString(), "G");
85	1	alleles = vc.getAlleles();
86	1	assertEquals(alleles.size(), 2);
87	1	assertTrue(alleles.get(0).isReference());
88	1	assertEquals(alleles.get(0).getBaseString(), "G");
89	1	assertFalse(alleles.get(1).isReference());
90	1	assertEquals(alleles.get(1).getBaseString(), "GA");
91
92		/*
93		* Deletion ACG -> A
94		*/
95	1	vc = variants.next();
96	1	assertFalse(vc.isSNP());
97	1	assertTrue(vc.isSimpleDeletion());
98	1	ref = vc.getReference();
99	1	assertEquals(ref.getBaseString(), "ACG");
100	1	alleles = vc.getAlleles();
101	1	assertEquals(alleles.size(), 2);
102	1	assertTrue(alleles.get(0).isReference());
103	1	assertEquals(alleles.get(0).getBaseString(), "ACG");
104	1	assertFalse(alleles.get(1).isReference());
105	1	assertEquals(alleles.get(1).getBaseString(), "A");
106
107	1	assertFalse(variants.hasNext());
108
109	1	variants.close();
110	1	reader.close();
111		}
112
113		/**
114		* Creates a temporary file to be read by the htsjdk VCF reader
115		*
116		* @return
117		* @throws IOException
118		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14
119	2	protected File writeVcfFile() throws IOException...
120		{
121	2	File f = File.createTempFile("Test", "vcf");
122	2	f.deleteOnExit();
123	2	PrintWriter pw = new PrintWriter(f);
124	2	for (String vcfLine : VCF)
125		{
126	10	pw.println(vcfLine);
127		}
128	2	pw.close();
129	2	return f;
130		}
131
132		/**
133		* A 'test' that demonstrates querying an indexed VCF file for features in a
134		* specified interval
135		*
136		* @throws IOException
137		*/
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09 1PASS
138	0	@Test...
139		public void testQuery_indexed() throws IOException
140		{
141		/*
142		* if not specified, assumes index file is filename.tbi
143		*/
144	0	VCFReader reader = new VCFReader(VCF_PATH);
145
146		/*
147		* gene NMT1 (human) is on chromosome 17
148		* GCHR38 (Ensembl): 45051610-45109016
149		* GCHR37 (gnoMAD): 43128978-43186384
150		* CDS begins at offset 9720, first CDS variant at offset 9724
151		*/
152	0	CloseableIterator<VariantContext> features = reader.query("17",
153		43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
154
155	0	assertEquals(printNext(features), 43138702);
156	0	assertEquals(printNext(features), 43138704);
157	0	assertEquals(printNext(features), 43138707);
158	0	assertEquals(printNext(features), 43138708);
159	0	assertEquals(printNext(features), 43138710);
160	0	assertEquals(printNext(features), 43138711);
161	0	assertFalse(features.hasNext());
162
163	0	features.close();
164	0	reader.close();
165		}
166
167		/**
168		* Prints the toString value of the next variant, and returns its start
169		* location
170		*
171		* @param features
172		* @return
173		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
174	0	protected int printNext(CloseableIterator<VariantContext> features)...
175		{
176	0	VariantContext next = features.next();
177	0	System.out.println(next.toString());
178	0	return next.getStart();
179		}
180
181		// "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
182
183		/**
184		* Test the query method that wraps a non-indexed VCF file
185		*
186		* @throws IOException
187		*/
		100% Uncovered Elements: 0 (18) Complexity: 1 Complexity Density: 0.06 1PASS
188	1	@Test(groups = "Functional")...
189		public void testQuery_plain() throws IOException
190		{
191	1	File f = writeVcfFile();
192	1	VCFReader reader = new VCFReader(f.getAbsolutePath());
193
194		/*
195		* query for overlap of 5-8 - should find variant at 7
196		*/
197	1	CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
198
199		/*
200		* INDEL G/GA variant
201		*/
202	1	VariantContext vc = variants.next();
203	1	assertTrue(vc.isIndel());
204	1	assertEquals(vc.getStart(), 7);
205	1	assertEquals(vc.getEnd(), 7);
206	1	Allele ref = vc.getReference();
207	1	assertEquals(ref.getBaseString(), "G");
208	1	List<Allele> alleles = vc.getAlleles();
209	1	assertEquals(alleles.size(), 2);
210	1	assertTrue(alleles.get(0).isReference());
211	1	assertEquals(alleles.get(0).getBaseString(), "G");
212	1	assertFalse(alleles.get(1).isReference());
213	1	assertEquals(alleles.get(1).getBaseString(), "GA");
214
215	1	assertFalse(variants.hasNext());
216
217	1	variants.close();
218	1	reader.close();
219		}
220		}