Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.GenotypeBuilder.alleles()

91
92
93
94
95
96
97
98
99
100
101
    @Test
    public void testMinMedian() {
        //TODO - might be better to make this test use a data provider?
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
        gb.alleles(vc.getAlleles());

        int pos = vc.getStart();
        band.add(pos++, gb.DP(10).GQ(11).PL(new int[]{0,11,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        assertValues(band, 10, 10, 11, 11);
View Full Code Here
123
124
125
126
127
128
129
130
131
132
133
    @Test
    public void testBigGQIsCapped() {
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
        gb.alleles(vc.getAlleles());

        band.add(vc.getStart(), gb.DP(1000).GQ(1000).PL(new int[]{0,10,100}).make());
        assertValues(band, 1000, 1000, 99, 99);
    }
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.