<commit_before>import java.util.Vector;
import java.io.IOException;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.io.File;

public class RemoteBedfileData extends RemoteBinaryData {

    RemoteBedfileData(DataClient dc, int numInds, MarkerData md, String collection) {
        super(dc, numInds, md, collection);
        bytesPerRecord = (int)Math.ceil(((double)numInds)/4);
    }


    public Vector<Byte> getRecord(String name)throws IOException{
        int snpIndex = md.getIndex(name,md.getSampleCollectionIndex(collection));

        if (snpIndex > -1){
            //ask data client to get this SNP
            dc.getSNPFiles(name,md.getChrom(name),collection,snpIndex,numInds);

            BedfileDataFile bed = new BedfileDataFile(dc.getLocalDir()+ File.separator+collection+"."+name+".bed",
                    this);

            return bed.getRecord(0);
        }else{
            return null;
        }
<commit_msg>added total number of snps to the list of values passed to the function that gets the single snp bnt and bed files to provide compatibility with Oxford intensity files<commit_after>import java.util.Vector;
import java.io.IOException;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.io.File;

public class RemoteBedfileData extends RemoteBinaryData {

    RemoteBedfileData(DataClient dc, int numInds, MarkerData md, String collection) {
        super(dc, numInds, md, collection);
        bytesPerRecord = (int)Math.ceil(((double)numInds)/4);
    }


    public Vector<Byte> getRecord(String name)throws IOException{
        int snpIndex = md.getIndex(name,md.getSampleCollectionIndex(collection));

        if (snpIndex > -1){
            //ask data client to get this SNP
            dc.getSNPFiles(name,md.getChrom(name),collection,snpIndex,numInds,totNumSNPs);

            BedfileDataFile bed = new BedfileDataFile(dc.getLocalDir()+ File.separator+collection+"."+name+".bed",
                    this);

            return bed.getRecord(0);
        }else{
            return null;
        }

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