BamStream

Class

BamStream

Class that provides an easy to use interface for reading and writing SAM and BAM files.

BamStream

Include Headers

seqan/bam_io.h

Data Members

bamIOContext	The BamIOContext object to use for reading and writing BamAlignmentRecords.
header	The BamHeader of the BamStream object.

Member Functions

BamStream

Constructor

Functions

atEnd	Check whether a BamStream object is at end when reading.
close	Close BamStream object's underlying file.
flush	Flush output when writing.
isGood	Check whether the BamStream object has is in the failure state.
open	Open a BamStream object for reading/writing.
readRecord	Read one BamAlignmentRecord from a BamStream.
reset	Reset BamStream object to status after construction.
writeRecord	Write one BamAlignmentRecord to a BamStream.

Examples

Stream through a SAM or BAM file.

seqan::BamStream bamIO("input.sam");

// Access the header through `header(bamIO)`;

seqan::BamAlignmentRecord record;
while (!atEnd(bamIO))
{
readRecord(record, bamIO);
// Process record...
}

Write out a string of SAM or BAM files.

seqan::BamStream("output.sam", seqan::BamStream::WRITE);

seqan::String<seqan::BamAlignmentRecord> records;
// Fill records string here.

// Set header through `header(bamIO)`.

for (unsigned i = 0; i < length(record); ++i)
writeRecord(bamIO, records[i]);

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