BufferedReader brSnpDetailFile = new BufferedReader(
                new InputStreamReader(new FileInputStream(
                        inputParameters.getAnnotationFilePath())));
        int index = 0;
        while ((stringLine = brSnpDetailFile.readLine()) != null) {
            String[] tempString = stringLine.split("\t", -1);
            /*server*/
            String snpId = tempString[3];
            String associatedGeneName = tempString[4];
            
            /*test
            String snpId = tempString[3];
            String associatedGeneName = tempString[5];
            */
            if (userSnpFileHashMap.containsKey(snpId)) {

                float pValue = userSnpFileHashMap.get(snpId);
                Snp snp = new Snp();
                snp.setAssociatedGeneName(associatedGeneName);
                snp.setReferenceId(snpId);
                snp.setPValue(pValue);

public void annotationFileParser(String filePath,String[] annotationFileArray){
        try {
            BufferedReader brAnnotation = new BufferedReader(
                    new InputStreamReader(new FileInputStream(new File(filePath))));

            String stringLine = null;
            int index = 0;
            while ((stringLine = brAnnotation.readLine()) != null) {
                annotationFileArray[index] = stringLine;
                index ++;
                if(index % 10000000 == 0){
                    System.out.println(index);
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }[/

int index = 0;
        for(int i = 0;i < annotationFileArray.length;i ++){
            
            /*server*/
            String snpId = annotationFileArray[i].split("\t", -1)[3];
            String associatedGeneName = annotationFileArray[i].split("\t", -1)[4];        
            /*
            String snpId = annotationFileArray[i].split("\t", -1)[3];
            String associatedGeneName = annotationFileArray[i].split("\t", -1)[5];
            */
            
            if (userSnpFileHashMap.containsKey(snpId)) {
                float pValue = userSnpFileHashMap.get(snpId);
                Snp snp = new Snp();
                snp.setAssociatedGeneName(associatedGeneName);
                snp.setReferenceId(snpId);
                snp.setPValue(pValue);
                
                // put all filtered snp into array.
                snpArrayList.add(snp);
                // put all filtered P-Value into array.
                pValueArrayList.add(pValue);
        
                if (!associateGeneNameIndexArrayHashMap
                        .containsKey(associatedGeneName)) {
                    ArrayList<Integer> tempArrayList = new ArrayList<Integer>();
                    tempArrayList.add(index);
                    associateGeneNameIndexArrayHashMap.put(associatedGeneName, tempArrayList);
                } else {
                    associateGeneNameIndexArrayHashMap.get(associatedGeneName).add(index);
                }
                index++;