Package org.broadinstitute.gatk.utils.locusiterator

Examples of org.broadinstitute.gatk.utils.locusiterator.LIBS_position


    @Test(dataProvider = "PileupElementTest")
    public void testPileupElementTest(LIBSTest params) {
        final GATKSAMRecord read = params.makeRead();
        final AlignmentStateMachine state = new AlignmentStateMachine(read);
        final LIBS_position tester = new LIBS_position(read);

        while ( state.stepForwardOnGenome() != null ) {
            tester.stepForwardOnGenome();
            final PileupElement pe = state.makePileupElement();

            Assert.assertEquals(pe.getRead(), read);
            Assert.assertEquals(pe.getMappingQual(), read.getMappingQuality());
            Assert.assertEquals(pe.getOffset(), state.getReadOffset());
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