@Override protected void setUp() { final int nPileupsToGenerate = 100; pileups = new ArrayList<ReadBackedPileup>(nPileupsToGenerate); SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); GenomeLocParser genomeLocParser; genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 50); final int readLen = 100; for ( int pileupN = 0; pileupN < nPileupsToGenerate; pileupN++ ) { ReadBackedPileup rbp = ArtificialSAMUtils.createReadBackedPileup(header, loc, readLen, insertSize, pileupSize); pileups.add(rbp); } }
/** * A unit test that creates an artificial read for testing some code that uses reads * * Note that effective creation of RBPs isn't so good. If you need pileups of specific properties, you shoud * look into building them yourself as in the example below */ @Test() public void testWithAPileup() { final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10); final ReadBackedPileup pileup = ArtificialSAMUtils.createReadBackedPileup(header, myLocation, 10, 400, 10); Assert.assertFalse(pileup.isEmpty()); // TODO -- add some tests here using pileup }