libStatGen Software 1
SamTags.h
1/*
2 * Copyright (C) 2010-2011 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#ifndef __SAM_TAGS_H__
19#define __SAM_TAGS_H__
20
21#include <stdint.h>
22#include <stdexcept>
23#include "SamRecord.h"
24
25/// Class for parsing/creating/operating on SAM/BAM record tags.
27{
28public:
29 ///////////////////////
30 /// @name Constants for parsing tags.
31 //@{
32 static const char* BQ_TAG;
33 static const char BQ_TAG_TYPE;
34 static const char* MD_TAG;
35 static const char MD_TAG_TYPE;
36 static const char* ORIG_POS_TAG;
37 static const char ORIG_POS_TAG_TYPE;
38 static const char* ORIG_CIGAR_TAG;
39 static const char ORIG_CIGAR_TAG_TYPE;
40 static const char* ORIG_QUAL_TAG;
41 static const char ORIG_QUAL_TAG_TYPE;
42 //@}
43
44 /// Create the MD tag for the specified input record and the genome.
45 /// \return returns true if an MD tag was created, false if one could not
46 /// be created.
47 static bool createMDTag(String& outputMDtag, SamRecord& inputRec, GenomeSequence& genome);
48 /// Check to see if the MD tag in the record is accurate.
49 static bool isMDTagCorrect(SamRecord& inputRec, GenomeSequence& genome);
50 // Update/Add the MD tag in the inputRec.
51 static bool updateMDTag(SamRecord& inputRec, GenomeSequence& genome);
52
53private:
54 SamTags();
55};
56
57
58#endif
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition: SamRecord.h:52
Class for parsing/creating/operating on SAM/BAM record tags.
Definition: SamTags.h:27
static bool isMDTagCorrect(SamRecord &inputRec, GenomeSequence &genome)
Check to see if the MD tag in the record is accurate.
Definition: SamTags.cpp:126
static bool createMDTag(String &outputMDtag, SamRecord &inputRec, GenomeSequence &genome)
Create the MD tag for the specified input record and the genome.
Definition: SamTags.cpp:34