org.molgenis.data.vcf.utils

Class VcfUtils

java.lang.Object

org.molgenis.data.vcf.utils.VcfUtils

public class VcfUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	TAB

Constructor Summary

Constructors

Constructor and Description
VcfUtils()

Method Summary

Modifier and Type	Method and Description
static boolean	checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile, PrintWriter outputVCFWriter, List<AttributeMetaData> infoFields)
static boolean	checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile, PrintWriter outputVCFWriter, List<AttributeMetaData> infoFields, List<String> attributesToInclude) Checks for previous annotations
static String	convertToVCF(Entity vcfEntity)
static String	convertToVCF(Entity vcfEntity, List<String> attributesToInclude) Convert an vcfEntity to a VCF line Only output attributes that are in the attributesToInclude list, or all if attributesToInclude is empty
static String	createId(Entity vcfEntity) Creates a internal molgenis id from a vcf entity
static List<AttributeMetaData>	getAtomicAttributesFromList(Iterable<AttributeMetaData> outputAttrs)
static HashMap<String,Trio>	getPedigree(File inputVcfFile) Get pedigree data from VCF Now only support child, father, mother No fancy data structure either Output: result.put(childID, Arrays.asList(new String[]{motherID, fatherID}));

Methods inherited from class java.lang.Object

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

Field Detail

TAB

public static final String TAB

See Also:

Constant Field Values

Constructor Detail

VcfUtils

public VcfUtils()

Method Detail

createId

public static String createId(Entity vcfEntity)

Creates a internal molgenis id from a vcf entity

Parameters:

vcfEntity -

Returns:

the id

convertToVCF

public static String convertToVCF(Entity vcfEntity)
                           throws MolgenisDataException

Throws:

MolgenisDataException

convertToVCF

public static String convertToVCF(Entity vcfEntity,
                                  List<String> attributesToInclude)
                           throws MolgenisDataException

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

Parameters:

vcfEntity -

attributesToInclude -

Returns:

Throws:

Exception

MolgenisDataException

checkPreviouslyAnnotatedAndAddMetadata

public static boolean checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile,
                                                             PrintWriter outputVCFWriter,
                                                             List<AttributeMetaData> infoFields)
                                                      throws FileNotFoundException,
                                                             MolgenisInvalidFormatException

Throws:

FileNotFoundException

MolgenisInvalidFormatException

checkPreviouslyAnnotatedAndAddMetadata

public static boolean checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile,
                                                             PrintWriter outputVCFWriter,
                                                             List<AttributeMetaData> infoFields,
                                                             List<String> attributesToInclude)
                                                      throws MolgenisInvalidFormatException,
                                                             FileNotFoundException

Checks for previous annotations

Parameters:

inputVcfFile -

outputVCFWriter -

infoFields -

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

Returns:

Throws:

Exception

MolgenisInvalidFormatException

FileNotFoundException

getAtomicAttributesFromList

public static List<AttributeMetaData> getAtomicAttributesFromList(Iterable<AttributeMetaData> outputAttrs)

getPedigree

public static HashMap<String,Trio> getPedigree(File inputVcfFile)
                                        throws FileNotFoundException

Get pedigree data from VCF Now only support child, father, mother No fancy data structure either Output: result.put(childID, Arrays.asList(new String[]{motherID, fatherID}));

Parameters:

inputVcfFile -

Returns:

Throws:

FileNotFoundException