1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
|
/*
* Copyright (C) 2012 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __SAM_RECORD_HELPER_H__
#define __SAM_RECORD_HELPER_H__
#include "SamRecord.h"
/// Class for extracting information from a SAM Flag.
class SamRecordHelper
{
public:
/// Helper method that checks if the record's read sequence starting
/// at the specified 0-based reference position matches the passed in
/// sequence.
/// \return returns -1 if it does not match,
/// returns the cycle (read position) of pos0Based if it does match.
static int checkSequence(SamRecord& record, int32_t pos0Based,
const char* sequence);
/// Helper to append the SAM string representation of all the tags to
/// the specified string. Does NOT add a preceding delimiter before the
/// first tag.
/// \param record record whose tags to append.
/// \param returnString string to append the tags to.
/// \param delim delimiter to use to separate different tags.
/// \return true on success, false on failure/partial generation.
static bool genSamTagsString(SamRecord& record, String& returnString,
char delim = '\t');
/// Helper to append the SAM string representation of the specified tag to
/// the specified string.
/// \param tag the tag name.
/// \param vtype the vtype.
/// \param value pointer to the value of the tag (will be cast
/// to int, double, char, or string based on vtype).
/// \param returnString string to append the tag to.
/// \return true on success, false on failure/partial generation.
static bool genSamTagString(const char* tag, char vtype,
void* value, String& returnString);
private:
SamRecordHelper();
};
#endif
|
