libStatGen Software 1
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PileupElementBaseQual.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
18#ifndef __PILEUP_ELEMENT_BASE_QUAL_H__
19#define __PILEUP_ELEMENT_BASE_QUAL_H__
20
21#include <stdint.h>
22#include "PileupElement.h"
23
24/// This class inherits from the base class and stores base and qualities.
26{
27public:
29 // NOTE that this method does not actually copy, it just resets.
31 virtual ~PileupElementBaseQual();
32
33 // Add an entry to this pileup element.
34 virtual void addEntry(SamRecord& record);
35
36 // Perform the alalysis associated with this class. In this case, it is
37 // a print of the base & quality information associated with this position.
38 virtual void analyze();
39
40 // Resets the entry, setting the new position associated with this element.
41 virtual void reset(int32_t refPosition);
42
43private:
44 static const char UNSET_QUAL = 0xFF;
45
46 char* myBases;
47 char* myQualities;
48 int myAllocatedSize;
49 int myIndex;
50 bool myAddDelAsBase;
51};
52
53#endif
This class inherits from the base class and stores base and qualities.
virtual void reset(int32_t refPosition)
Resets the entry, setting the new position associated with this element.
virtual void analyze()
Perform the analysis associated with this class.
virtual void addEntry(SamRecord &record)
Add an entry to this pileup element.
This is a base class pileup component, representing the information for one reference position.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition SamRecord.h:52