/* (non-Javadoc)
  * @see org.genomesmanager.services.impl.snps.SnpsImporter#parseMipsSnps(java.util.List)
  */
 @Override
 public void parseMipsSnps(List<String> lines) {
   System.out.println("Lines: " + lines.size());
   int lineN = 1;
   for (String line : lines) {
     String[] elems = line.split("\t+");
     String scaffoldName = elems[0];
     Sequence seq = sequenceRepository.findLatest(scaffoldName);
     if (seq == null) {
       errors.add(lineN + "\t" + line + "\t" + "Scaffold " + scaffoldName + " not found");
       continue;
     }
     int pos = Integer.parseInt(elems[1]);
     String referenceNucl = elems[2];
     for (int i = 3; i < elems.length; i++) {
       String reseq = elems[i];
       if (!reseq.equals("?")) {
         Snp snp = new Snp();
         snp.setIndividual(individuals.get(i - 3));
         snp.setPos(pos);
         snp.setSequence(seq);
         snp.setReference(referenceNucl);
         snp.setReseq(reseq);
         snps.add(snp);
       }
     }
     if (lineN % 1000 == 0) {
       System.out.println("Done " + lineN + " of " + lines.size());
     }
     lineN++;
   }
 }