diff --git a/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java b/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java index c2e3039..05081ec 100644 --- a/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java +++ b/test/org/broadinstitute/cga/tools/gatk/walkers/cancer/mutect/MuTectWalkerUnitTest.java @@ -30,23 +30,11 @@ public class MuTectWalkerUnitTest extends BaseTest { public byte ref = 'A'; public byte alt = 'T'; - // example genome loc parser for this test, can be deleted if you don't use the reference - private GenomeLocParser genomeLocParser; - - // example fasta index file, can be deleted if you don't use the reference - private IndexedFastaSequenceFile seq; - - @BeforeClass - public void setup() throws FileNotFoundException { - // sequence - seq = new CachingIndexedFastaSequenceFile(new File(hg19Reference)); - genomeLocParser = new GenomeLocParser(seq); - } - @Test public void basicPileupTest() { - final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); - final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10); + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(5, 1, 10000); + GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("chr1", 10); final int pileupSize = 100; final int readLength = 10;