Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
VCFReader	16	41	27	20	0.746835574.7%	Show methods

Class VCFReader

Class VCFReader	Line # 16	Total Statements 41	Complexity 27	Uncovered Elements 20	TOTAL Coverage 0.746835574.7%
VCFReader(String)   VCFReader(String)	3636	7.07	4.04	8.08	0.3846154 0.384615438.5%
close() : void   close() : void	5454	2.02	2.02	1.01	0.75 0.7575%
iterator() : CloseableIterator<VariantContext>   iterator() : CloseableIterator<VariantContext>	6767	1.01	2.02	1.01	0.6666667 0.666666766.7%
query(String,int,int) : CloseableIterator<VariantContext>   query(String,int,int) : CloseableIterator<VariantContext>	8888	5.05	3.03	4.04	0.5555556 0.555555655.6%
findNext() : VariantContext   findNext() : VariantContext	126126	14.014	7.07	2.02	0.90909094 0.9090909490.9%
hasNext() : boolean   hasNext() : boolean	157157	4.04	2.02	0.00	1.0 1.0100%
next() : VariantContext   next() : VariantContext	168168	3.03	1.01	0.00	1.0 1.0100%
remove() : void   remove() : void	180180	0.00	1.01	0.00	-1.0 -1.0 -
close() : void   close() : void	186186	1.01	1.01	0.00	1.0 1.0100%
queryUnindexed(String,int,int) : CloseableIterator<VariantContext>   queryUnindexed(String,int,int) : CloseableIterator<VariantContext>	114114	2.02	1.01	0.00	1.0 1.0100%
getFileHeader() : VCFHeader   getFileHeader() : VCFHeader	199199	1.01	2.02	1.01	0.6666667 0.666666766.7%
isIndex() : boolean   isIndex() : boolean	210210	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.70886075	jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq	1PASS
	0.65822786	jalview.io.vcf.VCFLoaderTest.testDoLoadjalview.io.vcf.VCFLoaderTest.testDoLoad	1PASS
	0.65822786	jalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrandjalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrand	1PASS
	0.65822786	jalview.io.vcf.VCFLoaderTest.testLoadVCFContigjalview.io.vcf.VCFLoaderTest.testLoadVCFContig	1PASS
	0.6075949	jalview.ext.htsjdk.VCFReaderTest.testQuery_plainjalview.ext.htsjdk.VCFReaderTest.testQuery_plain	1PASS
	0.16455697	jalview.ext.htsjdk.VCFReaderTest.testReadVcf_plainjalview.ext.htsjdk.VCFReaderTest.testReadVcf_plain	1PASS

 

Source view

1		package jalview.ext.htsjdk;
2
3		import htsjdk.samtools.util.CloseableIterator;
4		import htsjdk.variant.variantcontext.VariantContext;
5		import htsjdk.variant.vcf.VCFFileReader;
6		import htsjdk.variant.vcf.VCFHeader;
7
8		import java.io.Closeable;
9		import java.io.File;
10		import java.io.IOException;
11
12		/**
13		* A thin wrapper for htsjdk classes to read either plain, or compressed, or
14		* compressed and indexed VCF files
15		*/
		74.7% Uncovered Elements: 20 (79) Complexity: 27 Complexity Density: 0.66
16		public class VCFReader implements Closeable, Iterable<VariantContext>
17		{
18		private static final String GZ = "gz";
19
20		private static final String TBI_EXTENSION = ".tbi";
21
22		private boolean indexed;
23
24		private VCFFileReader reader;
25
26		/**
27		* Constructor given a raw or compressed VCF file or a (tabix) index file
28		* <p>
29		* For now, file type is inferred from its suffix: .gz or .bgz for compressed
30		* data, .tbi for an index file, anything else is assumed to be plain text
31		* VCF.
32		*
33		* @param f
34		* @throws IOException
35		*/
		38.5% Uncovered Elements: 8 (13) Complexity: 4 Complexity Density: 0.57
36	6	public VCFReader(String filePath) throws IOException...
37		{
38	6	if (filePath.endsWith(GZ))
39		{
40	0	if (new File(filePath + TBI_EXTENSION).exists())
41		{
42	0	indexed = true;
43		}
44		}
45	6	else if (filePath.endsWith(TBI_EXTENSION))
46		{
47	0	indexed = true;
48	0	filePath = filePath.substring(0, filePath.length() - 4);
49		}
50
51	6	reader = new VCFFileReader(new File(filePath), indexed);
52		}
53
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
54	5	@Override...
55		public void close() throws IOException
56		{
57	5	if (reader != null)
58		{
59	5	reader.close();
60		}
61		}
62
63		/**
64		* Returns an iterator over VCF variants in the file. The client should call
65		* close() on the iterator when finished with it.
66		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
67	1	@Override...
68		public CloseableIterator<VariantContext> iterator()
69		{
70	1	return reader == null ? null : reader.iterator();
71		}
72
73		/**
74		* Queries for records overlapping the region specified. Note that this method
75		* is performant if the VCF file is indexed, and may be very slow if it is
76		* not.
77		* <p>
78		* Client code should call close() on the iterator when finished with it.
79		*
80		* @param chrom
81		* the chromosome to query
82		* @param start
83		* query interval start
84		* @param end
85		* query interval end
86		* @return
87		*/
		55.6% Uncovered Elements: 4 (9) Complexity: 3 Complexity Density: 0.6
88	40	public CloseableIterator<VariantContext> query(final String chrom,...
89		final int start, final int end)
90		{
91	40	if (reader == null) {
92	0	return null;
93		}
94	40	if (indexed)
95		{
96	0	return reader.query(chrom, start, end);
97		}
98		else
99		{
100	40	return queryUnindexed(chrom, start, end);
101		}
102		}
103
104		/**
105		* Returns an iterator over variant records read from a flat file which
106		* overlap the specified chromosomal positions. Call close() on the iterator
107		* when finished with it!
108		*
109		* @param chrom
110		* @param start
111		* @param end
112		* @return
113		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
114	40	protected CloseableIterator<VariantContext> queryUnindexed(...
115		final String chrom, final int start, final int end)
116		{
117	40	final CloseableIterator<VariantContext> it = reader.iterator();
118
119	40	return new CloseableIterator<VariantContext>()
120		{
121		boolean atEnd = false;
122
123		// prime look-ahead buffer with next matching record
124		private VariantContext next = findNext();
125
		90.9% Uncovered Elements: 2 (22) Complexity: 7 Complexity Density: 0.5
126	69	private VariantContext findNext()...
127		{
128	69	if (atEnd)
129		{
130	0	return null;
131		}
132	69	VariantContext variant = null;
133	155	while (it.hasNext())
134		{
135	121	variant = it.next();
136	121	int vstart = variant.getStart();
137
138	121	if (vstart > end)
139		{
140	6	atEnd = true;
141	6	close();
142	6	return null;
143		}
144
145	115	int vend = variant.getEnd();
146		// todo what is the undeprecated way to get
147		// the chromosome for the variant?
148	115	if (chrom.equals(variant.getChr()) && (vstart <= end)
149		&& (vend >= start))
150		{
151	29	return variant;
152		}
153		}
154	34	return null;
155		}
156
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
157	68	@Override...
158		public boolean hasNext()
159		{
160	68	boolean hasNext = !atEnd && (next != null);
161	68	if (!hasNext)
162		{
163	40	close();
164		}
165	68	return hasNext;
166		}
167
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
168	29	@Override...
169		public VariantContext next()
170		{
171		/*
172		* return the next match, and then re-prime
173		* it with the following one (if any)
174		*/
175	29	VariantContext temp = next;
176	29	next = findNext();
177	29	return temp;
178		}
179
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
180	0	@Override...
181		public void remove()
182		{
183		// not implemented
184		}
185
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
186	86	@Override...
187		public void close()
188		{
189	86	it.close();
190		}
191		};
192		}
193
194		/**
195		* Returns an object that models the VCF file headers
196		*
197		* @return
198		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
199	4	public VCFHeader getFileHeader()...
200		{
201	4	return reader == null ? null : reader.getFileHeader();
202		}
203
204		/**
205		* Answers true if we are processing a tab-indexed VCF file, false if it is a
206		* plain text (uncompressed) file.
207		*
208		* @return
209		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
210	0	public boolean isIndex()...
211		{
212	0	return indexed;
213		}
214		}