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 char	ANNOTATION_FIELD_SEPARATOR
static String	EFFECT
static String	SPACE_PIPE_SEPERATOR
static String	VARIANT

Constructor Summary

Constructors

Constructor and Description
VcfWriterUtils()

Method Summary

Modifier and Type	Method and Description
static void	writeToVcf(Entity vcfEntity, List<AttributeMetaData> 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<AttributeMetaData> 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<AttributeMetaData> 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

ANNOTATION_FIELD_SEPARATOR

public static final char ANNOTATION_FIELD_SEPARATOR

See Also:

Constant Field Values

SPACE_PIPE_SEPERATOR

public static final String SPACE_PIPE_SEPERATOR

See Also:

Constant Field Values

Constructor Detail

VcfWriterUtils

public VcfWriterUtils()

Method Detail

writeVcfHeader

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

Checks for previous annotations

Parameters:

inputVcfFile -

outputVCFWriter -

addedAttributes -

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

Throws:

MolgenisInvalidFormatException

IOException

writeToVcf

public static void writeToVcf(Entity vcfEntity,
                              List<AttributeMetaData> 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