private void createBAM(final List<GATKSAMRecord> reads) throws IOException { testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam"); testBAM.deleteOnExit(); SAMFileWriter out = new SAMFileWriterFactory() .setCreateIndex(true) .makeBAMWriter(reads.get(0).getHeader(), true, testBAM); for (GATKSAMRecord read : reads) { out.addAlignment(read); } out.close(); new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit(); new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit(); }