org.molgenis.data.vcf.utils

Class VcfWriterUtils

java.lang.Object

org.molgenis.data.vcf.utils.VcfWriterUtils

public class VcfWriterUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	EFFECT
static String	VARIANT

Constructor Summary

Constructors

Constructor and Description
VcfWriterUtils()

Method Summary

Modifier and Type	Method and Description
static void	writeToVcf(Entity vcfEntity, BufferedWriter writer) Overload of writeToVcf to support a simpler call with only Entity and Writer.
static void	writeToVcf(Entity vcfEntity, List<Attribute> addedAttributes, List<String> attributesToInclude, BufferedWriter writer) Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty
static void	writeVcfHeader(File inputVcfFile, BufferedWriter outputVCFWriter, List<Attribute> addedAttributes) Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty
static void	writeVcfHeader(File inputVcfFile, BufferedWriter outputVCFWriter, List<Attribute> addedAttributes, List<String> attributesToInclude) Checks for previous annotations

Methods inherited from class java.lang.Object

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

Field Detail

VARIANT

public static final String VARIANT

See Also:

Constant Field Values

EFFECT

public static final String EFFECT

See Also:

Constant Field Values

Constructor Detail

VcfWriterUtils

public VcfWriterUtils()

Method Detail

writeVcfHeader

public static void writeVcfHeader(File inputVcfFile,
                                  BufferedWriter outputVCFWriter,
                                  List<Attribute> addedAttributes)
                           throws MolgenisInvalidFormatException,
                                  IOException

Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty

Parameters:

inputVcfFile -

outputVCFWriter -

addedAttributes -

Throws:

IOException,MolgenisInvalidFormatException

MolgenisInvalidFormatException

IOException

writeVcfHeader

public static void writeVcfHeader(File inputVcfFile,
                                  BufferedWriter outputVCFWriter,
                                  List<Attribute> addedAttributes,
                                  List<String> attributesToInclude)
                           throws MolgenisInvalidFormatException,
                                  IOException

Checks for previous annotations

Parameters:

inputVcfFile -

outputVCFWriter -

addedAttributes -

attributesToInclude - , the Attribute to write to the VCF file, if empty writes all attributes

Throws:

MolgenisInvalidFormatException

IOException

writeToVcf

public static void writeToVcf(Entity vcfEntity,
                              BufferedWriter writer)
                       throws MolgenisDataException,
                              IOException

Overload of writeToVcf to support a simpler call with only Entity and Writer.

Parameters:

vcfEntity -

writer -

Throws:

MolgenisDataException

IOException

writeToVcf

public static void writeToVcf(Entity vcfEntity,
                              List<Attribute> addedAttributes,
                              List<String> attributesToInclude,
                              BufferedWriter writer)
                       throws MolgenisDataException,
                              IOException

Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty

Parameters:

vcfEntity -

addedAttributes -

attributesToInclude -

writer -

Throws:

IOException,Exception

MolgenisDataException

IOException