VcfStream

Class

VcfStream

High-level VCF I/O class.

class VcfStream

Include Headers

seqan/vcf_io.h

Member Functions

Constructor.

Functions

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

Examples

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

1	#include <seqan/basic.h>
2	#include <seqan/vcf_io.h>
3
4	using namespace seqan;
5
6	// USAGE: vcf_stream_read IN.vcf
7	//
8	// Read VCF file and print the positions (reference, position) to stdout.
9
10	int main(int argc, char ** argv)
11	{
12	if (argc != 2)
13	{
14	std::cerr << "USAGE: " << argv[1] << " IN.vcf\n";
15	return 1;
16	}
17
18	VcfStream vcfIn(argv[1]);
19	if (!isGood(vcfIn))
20	{
21	std::cerr << "ERROR: Could not open " << argv[1] << " for reading!\n";
22	return 1;
23	}
24
25	VcfRecord record;
26	while (!atEnd(vcfIn))
27	{
28	if (readRecord(record, vcfIn) != 0)
29	{
30	std::cerr << "ERROR: Problem reading from " << argv[1] << "\n";
31	return 1;
32	}
33
34	// Note that we print the position 1-based since we use text output
35	// whereas it is 0-based in the VcfRecord.
36	std::cout << vcfIn.header.sequenceNames[record.rID]
37	<< "\t" << (record.beginPos + 1) << "\n";
38	}
39
40	return 0;
41	}

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