org.molgenis.data.vcf.utils

Class VcfUtils

java.lang.Object

org.molgenis.data.vcf.utils.VcfUtils

public class VcfUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
VcfUtils()

Method Summary

Modifier and Type	Method and Description
static List<Entity>	createEntityStructureForVcf(EntityMetaData entityMetaData, String attributeName, java.util.stream.Stream<Entity> inputStream)
static List<Entity>	createEntityStructureForVcf(EntityMetaData entityMetaData, String attributeName, java.util.stream.Stream<Entity> inputStream, List<AttributeMetaData> annotatorAttributes)
static String	createId(Entity vcfEntity) Creates a internal molgenis id from a vcf entity
static List<AttributeMetaData>	getAtomicAttributesFromList(Iterable<AttributeMetaData> outputAttrs)
static Map<String,AttributeMetaData>	getAttributesMapFromList(Iterable<AttributeMetaData> outputAttrs)
static String	getIdFromInfoField(String line)
static HashMap<String,Trio>	getPedigree(Scanner inputVcfFileScanner) 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}));
static Iterator<Entity>	reverseXrefMrefRelation(Iterator<Entity> annotatedRecords)
static String	toVcfDataType(MolgenisFieldTypes.FieldTypeEnum dataType)

Methods inherited from class java.lang.Object

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

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

getIdFromInfoField

public static String getIdFromInfoField(String line)

getAtomicAttributesFromList

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

getAttributesMapFromList

public static Map<String,AttributeMetaData> getAttributesMapFromList(Iterable<AttributeMetaData> outputAttrs)

toVcfDataType

public static String toVcfDataType(MolgenisFieldTypes.FieldTypeEnum dataType)

reverseXrefMrefRelation

public static Iterator<Entity> reverseXrefMrefRelation(Iterator<Entity> annotatedRecords)

createEntityStructureForVcf

public static List<Entity> createEntityStructureForVcf(EntityMetaData entityMetaData,
                                                       String attributeName,
                                                       java.util.stream.Stream<Entity> inputStream)

createEntityStructureForVcf

public static List<Entity> createEntityStructureForVcf(EntityMetaData entityMetaData,
                                                       String attributeName,
                                                       java.util.stream.Stream<Entity> inputStream,
                                                       List<AttributeMetaData> annotatorAttributes)

getPedigree

public static HashMap<String,Trio> getPedigree(Scanner inputVcfFileScanner)
                                        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:

inputVcfFileScanner -

Returns:

Throws:

FileNotFoundException