org.molgenis.data.annotation.core.utils

Class CmdLineAnnotatorUtils

java.lang.Object

org.molgenis.data.annotation.core.utils.CmdLineAnnotatorUtils

public class CmdLineAnnotatorUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
CmdLineAnnotatorUtils()

Method Summary

Modifier and Type	Method and Description
static String	annotate(RepositoryAnnotator annotator, VcfAttributes vcfAttributes, EntityTypeFactory entityTypeFactory, AttributeFactory attributeFactory, EffectStructureConverter effectStructureConverter, File inputVcfFile, File outputVCFFile, List<String> attributesToInclude, boolean update) Adds a new compound attribute to an existing CrudRepository

Methods inherited from class java.lang.Object

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

Constructor Detail

CmdLineAnnotatorUtils

public CmdLineAnnotatorUtils()

Method Detail

annotate

public static String annotate(RepositoryAnnotator annotator,
                              VcfAttributes vcfAttributes,
                              EntityTypeFactory entityTypeFactory,
                              AttributeFactory attributeFactory,
                              EffectStructureConverter effectStructureConverter,
                              File inputVcfFile,
                              File outputVCFFile,
                              List<String> attributesToInclude,
                              boolean update)
                       throws IOException,
                              MolgenisInvalidFormatException

Adds a new compound attribute to an existing CrudRepository

Parameters:

annotator - the annotator to be runned

vcfAttributes - utility class for vcf metadata

entityTypeFactory - factory for molgenis entityType

attributeFactory - factory for molgenis entityType

effectStructureConverter - utility class for converting a vcfRepo from and to the molgenis entity structure for "effects" annotations

inputVcfFile - the vcf file to be annotated

outputVCFFile - the resulting, annotated vcf file

attributesToInclude - the attributes of the annotator that should be written to the result

update - boolean indicating if values already present for the annotator attributes should be updated(true) or overwritten (false)

Returns:

the path of the result vcf file

Throws:

IOException

MolgenisInvalidFormatException