libStatGen Software 1
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BgzfFileType.cpp
1/*
2 * Copyright (C) 2010 Regents of the University of Michigan
3 *
4 * This program is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * This program is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */
17
18#ifdef __ZLIB_AVAILABLE__
19
20#include <iostream>
21#include <string.h>
22
23#include "BgzfFileType.h"
24
25// Default to require the EOF block at the end of the file.
26bool BgzfFileType::ourRequireEofBlock = true;
27
28BgzfFileType::BgzfFileType(const char * filename, const char * mode)
29{
30 // If the file is for write and is '-', then write to stdout.
31 if(((mode[0] == 'w') || (mode[0] == 'W')) &&
32 (strcmp(filename, "-") == 0))
33 {
34 // Write to stdout.
35 bgzfHandle = bgzf_dopen(fileno(stdout), mode);
36 }
37 else if(((mode[0] == 'r') || (mode[0] == 'R')) &&
38 (strcmp(filename, "-") == 0))
39 {
40 // read from stdin
41 bgzfHandle = bgzf_dopen(fileno(stdin), mode);
42 }
43 else
44 {
45 bgzfHandle = bgzf_open(filename, mode);
46 }
47
48 myStartPos = 0;
49 if (bgzfHandle != NULL)
50 {
51 // Check to see if the file is being opened for read, if the eof block
52 // is required, and if it is, if it is there.
53 if ((mode[0] == 'r' || mode[0] == 'R') && (strcmp(filename, "-") != 0)
54 && ourRequireEofBlock && (bgzf_check_EOF(bgzfHandle) != 1))
55 {
56 std::cerr << "BGZF EOF marker is missing in " << filename << std::endl;
57 // the block is supposed to be there, but isn't, so close the file.
58 close();
59 }
60 else
61 {
62 // Successfully opened a properly formatted file, so get the start
63 // position.
64 myStartPos = bgzf_tell(bgzfHandle);
65 }
66 }
67
68 myEOF = false;
69}
70
71
72// Set whether or not to require the EOF block at the end of the
73// file. True - require the block. False - do not require the block.
74void BgzfFileType::setRequireEofBlock(bool requireEofBlock)
75{
76 ourRequireEofBlock = requireEofBlock;
77}
78
79#endif