libStatGen Software 1
WriteFiles.h
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#ifndef __WRITE_FILES_H__
18#define __WRITE_FILES_H__
19
20#include <stdio.h>
21#include "GlfFile.h"
22
23
24void testWrite();
25void testHeaderWrite();
26void testWriteCopiedHeader();
27
29{
30public:
31 void testWrite();
32private:
33 void writeHeader(GlfFile& glfOut, int headerNum);
34 void writeRefSection1(GlfFile& glfOut);
35 void writeSec1Record1(GlfFile& glfOut);
36 void writeSec1Record2(GlfFile& glfOut);
37 void writeEndMarker(GlfFile& glfOut);
38 void writeRefSection2(GlfFile& glfOut);
39 void writeSec2Record1(GlfFile& glfOut);
40
41 void readHeader(GlfFile& glfIn, int headerNum);
42 void readRefSection1(GlfFile& glfIn);
43 void readSec1Record1(GlfFile& glfIn);
44 void readSec1Record2(GlfFile& glfIn);
45 void readEndMarker(GlfFile& glfIn);
46 void readRefSection2(GlfFile& glfIn);
47 void readSec2Record1(GlfFile& glfIn);
48
49 void checkEOF(GlfFile& glfIn);
50
51 // 1st file header values:
52 static const std::string HEADER_TEXT1;
53
54 // SEC1 values:
55 static const std::string SEC1_REFNAME;
56 static const uint32_t SEC1_REFLEN = 200;
57
58 // SEC1REC1 values:
59 static const uint8_t SEC1REC1_RECTYPE = 1;
60 static const uint8_t SEC1REC1_REFBASE = 4;
61 static const uint32_t SEC1REC1_OFFSET = 99;
62 static const uint32_t SEC1REC1_MINLK = 55;
63 static const uint32_t SEC1REC1_READDEPTH = 31;
64 static const uint8_t SEC1REC1_RMSMAPQ = 25;
65
66 // SEC1REC2 values:
67 static const uint8_t SEC1REC2_RECTYPE = 2;
68 static const uint8_t SEC1REC2_REFBASE = 1;
69 static const uint32_t SEC1REC2_OFFSET = 6;
70 static const uint32_t SEC1REC2_MINLK = 44;
71 static const uint32_t SEC1REC2_READDEPTH = 66;
72 static const uint8_t SEC1REC2_RMSMAPQ = 32;
73 static const uint8_t SEC1REC2_LKHOM1 = 98;
74 static const uint8_t SEC1REC2_LKHOM2 = 86;
75 static const uint8_t SEC1REC2_LKHET = 73;
76 static const int16_t SEC1REC2_INDELLEN1 = 2;
77 static const int16_t SEC1REC2_INDELLEN2 = -3;
78 static const std::string SEC1REC2_INDELSEQ1;
79 static const std::string SEC1REC2_INDELSEQ2;
80
81 // SEC2 values
82 static const std::string SEC2_REFNAME;
83 static const uint32_t SEC2_REFLEN = 102;
84
85 // SEC2REC1 values:
86 static const uint8_t SEC2REC1_RECTYPE = 1;
87 static const uint8_t SEC2REC1_REFBASE = 2;
88 static const uint32_t SEC2REC1_OFFSET = 50;
89 static const uint32_t SEC2REC1_MINLK = 55;
90 static const uint32_t SEC2REC1_READDEPTH = 31;
91 static const uint8_t SEC2REC1_RMSMAPQ = 25;
92
93 // 2nd file header.
94 static const std::string HEADER_TEXT2;
95 // 3rd file header.
96 static const std::string HEADER_TEXT3;
97};
98#endif
This class allows a user to easily read/write a GLF file.
Definition: GlfFile.h:29