Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
VCFReader	37	46	29	0.00%	Show methods

Class VCFReader

Class VCFReader	Line # 37	Total Statements 46	Complexity 29	TOTAL Coverage 0.00%
VCFReader(String)   VCFReader(String)	6060	12.012	6.06	0.0 0.00%
close() : void   close() : void	9393	2.02	2.02	0.0 0.00%
iterator() : CloseableIterator<VariantContext>   iterator() : CloseableIterator<VariantContext>	106106	1.01	2.02	0.0 0.00%
query(String,int,int) : CloseableIterator<VariantContext>   query(String,int,int) : CloseableIterator<VariantContext>	127127	5.05	3.03	0.0 0.00%
findNext() : VariantContext   findNext() : VariantContext	166166	14.014	7.07	0.0 0.00%
hasNext() : boolean   hasNext() : boolean	197197	4.04	2.02	0.0 0.00%
next() : VariantContext   next() : VariantContext	208208	3.03	1.01	0.0 0.00%
remove() : void   remove() : void	220220	0.00	1.01	-1.0 -1.0 -
close() : void   close() : void	226226	1.01	1.01	0.0 0.00%
queryUnindexed(String,int,int) : CloseableIterator<VariantContext>   queryUnindexed(String,int,int) : CloseableIterator<VariantContext>	154154	2.02	1.01	0.0 0.00%
getFileHeader() : VCFHeader   getFileHeader() : VCFHeader	239239	1.01	2.02	0.0 0.00%
isIndex() : boolean   isIndex() : boolean	250250	1.01	1.01	0.0 0.00%

 

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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 java.io.Closeable;
24		import java.io.File;
25		import java.io.IOException;
26
27		import htsjdk.samtools.util.CloseableIterator;
28		import htsjdk.variant.variantcontext.VariantContext;
29		import htsjdk.variant.vcf.VCFFileReader;
30		import htsjdk.variant.vcf.VCFHeader;
31		import jalview.bin.Console;
32
33		/**
34		* A thin wrapper for htsjdk classes to read either plain, or compressed, or
35		* compressed and indexed VCF files
36		*/
		0% Uncovered Elements: 86 (86) Complexity: 29 Complexity Density: 0.63
37		public class VCFReader implements Closeable, Iterable<VariantContext>
38		{
39		private static final String GZ = "gz";
40
41		private static final String TBI_EXTENSION = ".tbi";
42
43		private static final String CSI_EXTENSION = ".csi";
44
45		private boolean indexed;
46
47		private VCFFileReader reader;
48
49		/**
50		* Constructor given a raw or compressed VCF file or a (csi or tabix) index
51		* file
52		* <p>
53		* If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of
54		* these extensions gives a valid file path, open as indexed, else as
55		* unindexed.
56		*
57		* @param f
58		* @throws IOException
59		*/
		0% Uncovered Elements: 20 (20) Complexity: 6 Complexity Density: 0.5
60	0	public VCFReader(String filePath) throws IOException...
61		{
62	0	indexed = false;
63	0	if (filePath.endsWith(TBI_EXTENSION)
64		|| filePath.endsWith(CSI_EXTENSION))
65		{
66	0	indexed = true;
67	0	filePath = filePath.substring(0, filePath.length() - 4);
68		}
69	0	else if (new File(filePath + TBI_EXTENSION).exists())
70		{
71	0	indexed = true;
72		}
73	0	else if (new File(filePath + CSI_EXTENSION).exists())
74		{
75	0	indexed = true;
76		}
77
78		/*
79		* we pass the name of the unindexed file to htsjdk,
80		* with a flag to assert whether it is indexed
81		*/
82	0	File file = new File(filePath);
83	0	if (file.exists())
84		{
85	0	reader = new VCFFileReader(file, indexed);
86		}
87		else
88		{
89	0	Console.error("File not found: " + filePath);
90		}
91		}
92
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
93	0	@Override...
94		public void close() throws IOException
95		{
96	0	if (reader != null)
97		{
98	0	reader.close();
99		}
100		}
101
102		/**
103		* Returns an iterator over VCF variants in the file. The client should call
104		* close() on the iterator when finished with it.
105		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
106	0	@Override...
107		public CloseableIterator<VariantContext> iterator()
108		{
109	0	return reader == null ? null : reader.iterator();
110		}
111
112		/**
113		* Queries for records overlapping the region specified. Note that this method
114		* is performant if the VCF file is indexed, and may be very slow if it is
115		* not.
116		* <p>
117		* Client code should call close() on the iterator when finished with it.
118		*
119		* @param chrom
120		* the chromosome to query
121		* @param start
122		* query interval start
123		* @param end
124		* query interval end
125		* @return
126		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
127	0	public CloseableIterator<VariantContext> query(final String chrom,...
128		final int start, final int end)
129		{
130	0	if (reader == null)
131		{
132	0	return null;
133		}
134	0	if (indexed)
135		{
136	0	return reader.query(chrom, start, end);
137		}
138		else
139		{
140	0	return queryUnindexed(chrom, start, end);
141		}
142		}
143
144		/**
145		* Returns an iterator over variant records read from a flat file which
146		* overlap the specified chromosomal positions. Call close() on the iterator
147		* when finished with it!
148		*
149		* @param chrom
150		* @param start
151		* @param end
152		* @return
153		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
154	0	protected CloseableIterator<VariantContext> queryUnindexed(...
155		final String chrom, final int start, final int end)
156		{
157	0	final CloseableIterator<VariantContext> it = reader.iterator();
158
159	0	return new CloseableIterator<VariantContext>()
160		{
161		boolean atEnd = false;
162
163		// prime look-ahead buffer with next matching record
164		private VariantContext next = findNext();
165
		0% Uncovered Elements: 22 (22) Complexity: 7 Complexity Density: 0.5
166	0	private VariantContext findNext()...
167		{
168	0	if (atEnd)
169		{
170	0	return null;
171		}
172	0	VariantContext variant = null;
173	0	while (it.hasNext())
174		{
175	0	variant = it.next();
176	0	int vstart = variant.getStart();
177
178	0	if (vstart > end)
179		{
180	0	atEnd = true;
181	0	close();
182	0	return null;
183		}
184
185	0	int vend = variant.getEnd();
186		// todo what is the undeprecated way to get
187		// the chromosome for the variant?
188	0	if (chrom.equals(variant.getContig()) && (vstart <= end)
189		&& (vend >= start))
190		{
191	0	return variant;
192		}
193		}
194	0	return null;
195		}
196
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
197	0	@Override...
198		public boolean hasNext()
199		{
200	0	boolean hasNext = !atEnd && (next != null);
201	0	if (!hasNext)
202		{
203	0	close();
204		}
205	0	return hasNext;
206		}
207
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
208	0	@Override...
209		public VariantContext next()
210		{
211		/*
212		* return the next match, and then re-prime
213		* it with the following one (if any)
214		*/
215	0	VariantContext temp = next;
216	0	next = findNext();
217	0	return temp;
218		}
219
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
220	0	@Override...
221		public void remove()
222		{
223		// not implemented
224		}
225
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
226	0	@Override...
227		public void close()
228		{
229	0	it.close();
230		}
231		};
232		}
233
234		/**
235		* Returns an object that models the VCF file headers
236		*
237		* @return
238		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
239	0	public VCFHeader getFileHeader()...
240		{
241	0	return reader == null ? null : reader.getFileHeader();
242		}
243
244		/**
245		* Answers true if we are processing a tab-indexed VCF file, false if it is a
246		* plain text (uncompressed) file.
247		*
248		* @return
249		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
250	0	public boolean isIndex()...
251		{
252	0	return indexed;
253		}
254		}