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#include <seqan/basic.h>
#include <seqan/bam_io.h>
//![bamRecord]
//![BamTagsDict]
using namespace seqan2;
//![BamTagsDict]
class myBamAlignmentRecord
{
public:
CharString qName; // QNAME
uint16_t flag; // FLAG
int32_t rID; // REF
int32_t beginPos; // POS
uint8_t mapQ; // MAPQ mapping quality, 255 for */invalid
uint16_t bin; // bin for indexing
String<CigarElement<> > cigar; // CIGAR string
int32_t rNextId; // RNEXT (0-based)
int32_t pNext; // PNEXT (0-based)
int32_t tLen; // TLEN
CharString seq; // SEQ, as in SAM/BAM file.
CharString qual; // Quality string as in SAM (Phred).
CharString tags; // Tags, raw as in BAM.
// Constants for marking pos, reference id and length members invalid (== 0/*).
static int32_t const INVALID_POS = -1;
static int32_t const INVALID_REFID = -1;
static int32_t const INVALID_LEN = 0;
};
//![bamRecord]
int main()
{
//![BamTagsDict]
BamAlignmentRecord record;
BamTagsDict tagsDict(record.tags);
//![BamTagsDict]
//![addTag]
setTagValue(tagsDict, "NM", 2);
// => tags: "NM:i:2"
setTagValue(tagsDict, "NH", 1);
// => tags: "NM:i:2 NH:i:1"
setTagValue(tagsDict, "NM", 3);
// => tags: "NM:i:3 NH:i:1"
//![addTag]
//![getIndex]
unsigned tagIdx = 0;
if (!findTagKey(tagIdx, tagsDict, "NH"))
std::cerr << "ERROR: Unknown key!\n";
//![getIndex]
//![extractValue]
int tagValInt = 0;
if (!extractTagValue(tagValInt, tagsDict, tagIdx))
std::cerr << "ERROR: There was an error extracting NH from tags!\n";
//![extractValue]
//![cast]
short tagValShort = 0;
extractTagValue(tagValShort, tagsDict, tagIdx);
//![cast]
return 0;
}
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