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 boolean	checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile, BufferedWriter outputVCFWriter, List<AttributeMetaData> infoFields)
static boolean	checkPreviouslyAnnotatedAndAddMetadata(File inputVcfFile, BufferedWriter outputVCFWriter, List<AttributeMetaData> infoFields, List<String> attributesToInclude) Checks for previous annotations
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}));
static void	writeToVcf(Entity vcfEntity, BufferedWriter writer)
static void	writeToVcf(Entity vcfEntity, 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

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

writeToVcf

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

Throws:

MolgenisDataException

IOException

writeToVcf

public static void writeToVcf(Entity vcfEntity,
                              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 -

attributesToInclude -

Throws:

IOException

Exception

MolgenisDataException

checkPreviouslyAnnotatedAndAddMetadata

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

Throws:

MolgenisInvalidFormatException

IOException

checkPreviouslyAnnotatedAndAddMetadata

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

Checks for previous annotations

Parameters:

inputVcfFile -

outputVCFWriter -

infoFields -

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

Returns:

Throws:

MolgenisInvalidFormatException

IOException

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