libStatGen Software 1
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SamRecordHelper.h
1/*
2 * Copyright (C) 2012 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_RECORD_HELPER_H__
19#define __SAM_RECORD_HELPER_H__
20
21#include "SamRecord.h"
22
23/// Class for extracting information from a SAM Flag.
25{
26public:
27
28 /// Helper method that checks if the record's read sequence starting
29 /// at the specified 0-based reference position matches the passed in
30 /// sequence.
31 /// \return returns -1 if it does not match,
32 /// returns the cycle (read position) of pos0Based if it does match.
33 static int checkSequence(SamRecord& record, int32_t pos0Based,
34 const char* sequence);
35
36 /// Helper to append the SAM string representation of all the tags to
37 /// the specified string. Does NOT add a preceding delimiter before the
38 /// first tag.
39 /// \param record record whose tags to append.
40 /// \param returnString string to append the tags to.
41 /// \param delim delimiter to use to separate different tags.
42 /// \return true on success, false on failure/partial generation.
43 static bool genSamTagsString(SamRecord& record, String& returnString,
44 char delim = '\t');
45
46
47 /// Helper to append the SAM string representation of the specified tag to
48 /// the specified string.
49 /// \param tag the tag name.
50 /// \param vtype the vtype.
51 /// \param value pointer to the value of the tag (will be cast
52 /// to int, double, char, or string based on vtype).
53 /// \param returnString string to append the tag to.
54 /// \return true on success, false on failure/partial generation.
55 static bool genSamTagString(const char* tag, char vtype,
56 void* value, String& returnString);
57
58private:
60};
61
62
63#endif
Class for extracting information from a SAM Flag.
static bool genSamTagString(const char *tag, char vtype, void *value, String &returnString)
Helper to append the SAM string representation of the specified tag to the specified string.
static bool genSamTagsString(SamRecord &record, String &returnString, char delim='\t')
Helper to append the SAM string representation of all the tags to the specified string.
static int checkSequence(SamRecord &record, int32_t pos0Based, const char *sequence)
Helper method that checks if the record's read sequence starting at the specified 0-based reference p...
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition SamRecord.h:52