org.seqdoop.hadoop_bam.util

Class VCFFileMerger

java.lang.Object

org.seqdoop.hadoop_bam.util.VCFFileMerger

public class VCFFileMerger
extends Object

Merges headerless VCF files produced by KeyIgnoringVCFOutputFormat into a single file. BCF files are not supported.

Constructor Summary

Constructors

Constructor and Description
VCFFileMerger()

Method Summary

Modifier and Type	Method and Description
static void	mergeParts(String partDirectory, String outputFile, htsjdk.variant.vcf.VCFHeader header) Merge part file shards produced by KeyIgnoringVCFOutputFormat into a single file with the given header.

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFFileMerger

public VCFFileMerger()

Method Detail

mergeParts

public static void mergeParts(String partDirectory,
                              String outputFile,
                              htsjdk.variant.vcf.VCFHeader header)
                       throws IOException

Merge part file shards produced by KeyIgnoringVCFOutputFormat into a single file with the given header.

Parameters:

partDirectory - the directory containing part files

outputFile - the file to write the merged file to

header - the header for the merged file

Throws:

IOException