Class BamHeaderRecord
Represents a header entry in a SAM file or the header section of the BAM header.

Defined in <seqan/bam_io.h>
Signature class BamHeaderRecord;

Member Function Overview

Member Typedef Overview

Member Variable Overview

Detailed Description

Remarks

Comment records are stored with one tag where the key is empty and the value is the comment.

Member Functions Detail

BamHeaderRecord::BamRecord();

Constructor.

Only the default constructor is provided.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

void clear(record);

Clear BamHeaderRecord object.

Parameters

record The record to clear.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

bool getTagValue(tagValue, idx, record); bool getTagValue(tagValue, key, record);

Return tag value from a BamHeaderRecord.

Parameters

tagValue The CharString to write the tag value to.
idx An integer with the index of the tag in the header record.
key A two-letter sequence with the key of the tag in the header record.

Returns

bool true in case the value could be retrieved, false otherwise.

Example

CharString tagValue;
bool keyFound = getTagValue(tagValue, "SN", record);

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

void setTagValue(idx, value, record); void setTagValue(key, value, record);

Sets the value of a tag in a BamHeaderRecord.

Parameters

idx The index of the tag in the header record to set the value for.
key The name of the tag (two-letter sequence) to set.
record The header record to set the value for.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Member Typedef Detail

BamHeaderRecord::TTag;

Type of the tag keys (Pair of TTagName and TTagValue).

BamHeaderRecord::TTagName;

Type of the tag keys (CharString).

BamHeaderRecord::TTags;

Type of the tags string (AllocString of TTag).

BamHeaderRecord::TTagValue;

Type of the tag values (CharString).

Member Variables Detail

TRecordString BamHeaderRecord::tags

The header record's tags, of type TTags.

BamHeaderRecordType BamHeaderRecord::type

Type of the record.