BCFReaderAdapter.java

package uk.ac.sanger.artemis.components.variant;

import java.io.IOException;
import java.util.List;

import org.apache.log4j.Logger;
import org.genedb.crawl.model.Gene;
import org.genedb.crawl.model.MappedVCFRecord;
import org.genedb.crawl.model.Sequence;

public class BCFReaderAdapter extends VariantReaderAdapter {
	
	private Logger logger = Logger.getLogger(BCFReaderAdapter.class);
	
	private BCFReader reader;
	
	public BCFReaderAdapter(String url) throws IOException {
		reader = new BCFReader(url);
		String hdr = reader.headerToString();
		logger.info(hdr);
	    if(hdr.indexOf("VCFv4") > -1) {
	    	reader.setVcf_v4(true);
	    }
		abstractReader = reader;
	}
	
	
	@Override
	public List<VCFRecord> unFilteredQuery(String region, int start, int end)
			throws IOException {
		
		List<VCFRecord> records = super.unFilteredQuery(region, start,end);
		
		if (records.size() <= 1) {
			logger.warn("running second time, suspicious size of 1.");
			records = super.unFilteredQuery(region, start,end);
		}
		
		return records;
	}
	
	@Override
	public List<MappedVCFRecord> query(
			String region, 
			int start, 
			int end, 
			List<CDSFeature> genes, 
			VariantFilterOptions options) throws IOException {
		
		List<MappedVCFRecord> records = super.query(region, start, end, genes, options);
		
		if (records.size() <= 1) {
			logger.warn("running second time, suspicious size of <= 1.");
			records = super.query(region, start, end, genes, options);
		}
		
		return records;
	          
	}


    @Override
    public void close() throws IOException {
        reader.close();
        reader = null;
    }
	
	
	
	
	


	
	
}