uk.ac.ebi.eva.pipeline.io.readers.AnnotationFlatFileReader.java Source code

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Here is the source code for uk.ac.ebi.eva.pipeline.io.readers.AnnotationFlatFileReader.java

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/*
 * Copyright 2016 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.eva.pipeline.io.readers;

import org.opencb.biodata.models.variant.annotation.VariantAnnotation;
import org.springframework.batch.item.file.FlatFileItemReader;
import org.springframework.core.io.Resource;

import uk.ac.ebi.eva.pipeline.io.GzipLazyResource;
import uk.ac.ebi.eva.pipeline.io.mappers.AnnotationLineMapper;
import java.io.File;

/**
 * Reader of VEP output annotation flat file. The file should be zipped.
 *
 * VEP output format:
 *
 *  20_60343_G/A   20:60343   A   -   -   -   intergenic_variant   -   -   -   -   -   -
 *  20_60419_A/G   20:60419   G   -   -   -   intergenic_variant   -   -   -   -   -   -
 *  20_60479_C/T   20:60479   T   -   -   -   intergenic_variant   -   -   -   -   -   rs149529999   GMAF=T:0.0018;AFR_MAF=T:0.01;AMR_MAF=T:0.0028
 *  ...
 *
 */
public class AnnotationFlatFileReader extends FlatFileItemReader<VariantAnnotation> {

    public AnnotationFlatFileReader(File file) {
        Resource resource = new GzipLazyResource(file);
        setResource(resource);
        setLineMapper(new AnnotationLineMapper());
    }

    public AnnotationFlatFileReader(String string) {
        this(new File(string));
    }
}