/* (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++; } }