htsjdk.variant.utils

Class VCFHeaderReader

java.lang.Object

htsjdk.variant.utils.VCFHeaderReader

public final class VCFHeaderReader
extends java.lang.Object

Utility class to read a VCF header without being told beforehand whether the input is VCF or BCF.

Method Summary

Modifier and Type	Method and Description
static VCFHeader	readHeaderFrom(SeekableStream in) Read a VCF header from a stream that may be a VCF file (possibly gzip or block compressed) or a BCF file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

readHeaderFrom

public static VCFHeader readHeaderFrom(SeekableStream in)
                                throws java.io.IOException

Read a VCF header from a stream that may be a VCF file (possibly gzip or block compressed) or a BCF file. After successfully reading a header the stream is positioned immediately after the header, otherwise, if an exception is thrown, the state of the stream is undefined.

Parameters:

in - the stream to read the header from

Returns:

the VCF header read from the stream

Throws:

TribbleException.InvalidHeader - if the header in the file is invalid

java.io.IOException - if an IOException occurs while reading the header