1 /*
2
3 dsh-compress Compression utility classes.
4 Copyright (c) 2014-2017 held jointly by the individual authors.
5
6 This library is free software; you can redistribute it and/or modify it
7 under the terms of the GNU Lesser General Public License as published
8 by the Free Software Foundation; either version 3 of the License, or (at
9 your option) any later version.
10
11 This library is distributed in the hope that it will be useful, but WITHOUT
12 ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
13 FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
14 License for more details.
15
16 You should have received a copy of the GNU Lesser General Public License
17 along with this library; if not, write to the Free Software Foundation,
18 Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
19
20 > http://www.fsf.org/licensing/licenses/lgpl.html
21 > http://www.opensource.org/licenses/lgpl-license.php
22
23 */
24 package org.dishevelled.compress;
25
26 import static com.google.common.base.Preconditions.checkNotNull;
27
28 import static org.dishevelled.compress.Compress.isBgzfFile;
29 import static org.dishevelled.compress.Compress.isBgzfInputStream;
30 import static org.dishevelled.compress.Compress.isBzip2File;
31 import static org.dishevelled.compress.Compress.isGzipFile;
32
33 import java.io.BufferedInputStream;
34 import java.io.BufferedReader;
35 import java.io.File;
36 import java.io.FileInputStream;
37 import java.io.FileReader;
38 import java.io.InputStream;
39 import java.io.InputStreamReader;
40 import java.io.IOException;
41
42 import javax.annotation.Nullable;
43
44 import htsjdk.samtools.util.BlockCompressedInputStream;
45
46 import org.apache.commons.compress.compressors.CompressorException;
47 import org.apache.commons.compress.compressors.CompressorStreamFactory;
48
49 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
50
51 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
52
53 /**
54 * File and input stream readers with support for bgzf, gzip, and bzip2 compression.
55 *
56 * @author Michael Heuer
57 */
58 public final class Readers
59 {
60
61 /**
62 * Private no-arg constructor.
63 */
64 private Readers()
65 {
66 // empty
67 }
68
69
70 /**
71 * Create and return a new buffered reader for the specified input stream.
72 *
73 * @since 1.1
74 * @param inputStream input stream, must not be null
75 * @return a new buffered reader for the specified input stream
76 * @throws IOException if an I/O error occurs
77 */
78 public static BufferedReader inputStreamReader(final InputStream inputStream) throws IOException
79 {
80 checkNotNull(inputStream);
81 return new BufferedReader(new InputStreamReader(inputStream));
82 }
83
84 /**
85 * Create and return a new buffered reader for the specified compressed file,
86 * autodetecting the compression type from the first few bytes of the file.
87 *
88 * @since 1.1
89 * @param file file, must not be null
90 * @return a new buffered reader for the specified file
91 * @throws IOException if an I/O error occurs
92 */
93 public static BufferedReader compressedFileReader(final File file) throws IOException
94 {
95 checkNotNull(file);
96 return compressedInputStreamReader(new FileInputStream(file));
97 }
98
99 /**
100 * Create and return a new buffered reader for the specified compressed input stream,
101 * autodetecting the compression type from the first few bytes of the stream.
102 *
103 * @since 1.1
104 * @param inputStream input stream, must not be null
105 * @return a new buffered reader for the specified input stream
106 * @throws IOException if an I/O error occurs
107 */
108 public static BufferedReader compressedInputStreamReader(final InputStream inputStream) throws IOException
109 {
110 checkNotNull(inputStream);
111 BufferedInputStream bufferedInputStream = inputStream instanceof BufferedInputStream ? (BufferedInputStream) inputStream : new BufferedInputStream(inputStream);
112 try
113 {
114 if (isBgzfInputStream(bufferedInputStream))
115 {
116 return bgzfInputStreamReader(bufferedInputStream);
117 }
118 return new BufferedReader(new InputStreamReader(new CompressorStreamFactory().createCompressorInputStream(bufferedInputStream)));
119 }
120 catch (CompressorException e)
121 {
122 // fall back to uncompressed input stream reader
123 return inputStreamReader(bufferedInputStream);
124 }
125 }
126
127 /**
128 * Create and return a new buffered reader for the specified block compressed gzip (BGZF) compressed file.
129 *
130 * @since 1.2
131 * @param file bgzf compressed file, must not be null
132 * @return a new buffered reader for the specified block compressed gzip (BGZF) compressed file
133 * @throws IOException if an I/O error occurs
134 */
135 public static BufferedReader bgzfFileReader(final File file) throws IOException
136 {
137 checkNotNull(file);
138 return new BufferedReader(new InputStreamReader(new BlockCompressedInputStream(file)));
139 }
140
141 /**
142 * Create and return a new buffered reader for the specified block compressed gzip (BGZF) compressed input stream.
143 *
144 * @since 1.2
145 * @param inputStream bgzf compressed input stream, must not be null
146 * @return a new buffered reader for the specified block compressed gzip (BGZF) compressed input stream
147 * @throws IOException if an I/O error occurs
148 */
149 public static BufferedReader bgzfInputStreamReader(final InputStream inputStream) throws IOException
150 {
151 checkNotNull(inputStream);
152 return new BufferedReader(new InputStreamReader(new BlockCompressedInputStream(inputStream)));
153 }
154
155 /**
156 * Create and return a new buffered reader for the specified gzip compressed file.
157 *
158 * @since 1.1
159 * @param file gzip compressed file, must not be null
160 * @return a new buffered reader for the specified gzip compressed file
161 * @throws IOException if an I/O error occurs
162 */
163 public static BufferedReader gzipFileReader(final File file) throws IOException
164 {
165 checkNotNull(file);
166 return gzipInputStreamReader(new FileInputStream(file));
167 }
168
169 /**
170 * Create and return a new buffered reader for the specified gzip compressed input stream.
171 *
172 * @param inputStream gzip compressed input stream, must not be null
173 * @return a new buffered reader for the specified gzip compressed input stream
174 * @throws IOException if an I/O error occurs
175 */
176 public static BufferedReader gzipInputStreamReader(final InputStream inputStream) throws IOException
177 {
178 checkNotNull(inputStream);
179 return new BufferedReader(new InputStreamReader(new GzipCompressorInputStream(inputStream)));
180 }
181
182 /**
183 * Create and return a new buffered reader for the specified bzip2 compressed file.
184 *
185 * @since 1.1
186 * @param file bzip2 compressed file, must not be null
187 * @return a new buffered reader for the specified bzip2 compressed file
188 * @throws IOException if an I/O error occurs
189 */
190 public static BufferedReader bzip2FileReader(final File file) throws IOException
191 {
192 checkNotNull(file);
193 return bzip2InputStreamReader(new FileInputStream(file));
194 }
195
196 /**
197 * Create and return a new buffered reader for the specified bzip2 compressed input stream.
198 *
199 * @param inputStream bzip2 compressed input stream, must not be null
200 * @return a new buffered reader for the specified bzip2 compressed input stream
201 * @throws IOException if an I/O error occurs
202 */
203 public static BufferedReader bzip2InputStreamReader(final InputStream inputStream) throws IOException
204 {
205 checkNotNull(inputStream);
206 return new BufferedReader(new InputStreamReader(new BZip2CompressorInputStream(inputStream)));
207 }
208
209 /**
210 * Create and return a new buffered reader with support for bgzf, gzip, or bzip2 compression for the specified file
211 * or <code>stdin</code> if the file is null.
212 *
213 * @param file file, if any
214 * @return a new buffered reader with support for bgzf, gzip, or bzip2 compression for the specified file
215 * or <code>stdin</code> if the file is null
216 * @throws IOException if an I/O error occurs
217 */
218 public static BufferedReader reader(@Nullable final File file) throws IOException
219 {
220 if (file == null)
221 {
222 return compressedInputStreamReader(System.in);
223 }
224 else if (isBgzfFile(file))
225 {
226 return bgzfFileReader(file);
227 }
228 else if (isGzipFile(file))
229 {
230 return gzipFileReader(file);
231 }
232 else if (isBzip2File(file))
233 {
234 return bzip2FileReader(file);
235 }
236 return new BufferedReader(new FileReader(file));
237 }
238 }