@Override public boolean run() { for (Gene g : config.getSnpEffectPredictor().getGenome().getGenes()) { // System.out.println(g.getGeneName()); for (Transcript tr : g) { if (!tr.isProteinCoding()) continue; if (tr.introns().size() < 2) continue; // System.out.println("\t" + tr.getId()); for (Intron i : tr.introns()) { int pos = i.getStart() + (int) (Math.random() * (i.size() - 2)) + 1; String line = i.getChromosomeName() + "\t" + pos + "\t.\tA\tT\t.\t.\tAC=1;GENE=" + g.getGeneName() + ";TR=" + tr.getId() + ";INTRON=" + i.getRank(); System.out.println(line); sb.append(line + "\n"); } } } Gpr.toFile(Gpr.HOME + "/introns_test.vcf", sb); return true; }