BedStream

Class

BedStream

High-level BED I/O class.

class BedStream

Include Headers

seqan/bed_io.h

Data Members

The names of the sequences (StringSet of CharString), updated when new sequences are seen in BED file.

Member Functions

Constructor.

Functions

addSequenceName	Add the name of a sequence to a BedStream.
atEnd	Query a BedStream for being at the end of the file.
close	Closes a BedStream
flush	Flush to a BedStream
isGood	Query a BedStream for errors.
open	Open a BedStream.
readRecord	Read a record from a BedStream
writeRecord	Write a record to a BedStream

Examples

The following example demonstrates reading a BED file and printing the variant locations.

1	#include <seqan/basic.h>
2	#include <seqan/bed_io.h>
3
4	using namespace seqan;
5
6	// USAGE: bed_stream_read IN.bed
7	//
8	// Read BED file and print the positions (reference, position) to stdout.
9	//
10	// We only read BED 3 here but the example can be easily adjusted to more complex examples.
11
12	int main(int argc, char ** argv)
13	{
14	if (argc != 2)
15	{
16	std::cerr << "USAGE: " << argv[1] << " IN.bed\n";
17	return 1;
18	}
19
20	BedStream bedIn(argv[1]);
21	if (!isGood(bedIn))
22	{
23	std::cerr << "ERROR: Could not open " << argv[1] << " for reading!\n";
24	return 1;
25	}
26
27	BedRecord<Bed3> record;
28	while (!atEnd(bedIn))
29	{
30	if (readRecord(record, bedIn) != 0)
31	{
32	std::cerr << "ERROR: Problem reading from " << argv[1] << "\n";
33	return 1;
34	}
35
36	std::cout << record.ref << "\t" << record.beginPos << "\n";
37	}
38
39	return 0;
40	}