List of makePileupElement() Examples

Examples of makePileupElement()

org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine.makePileupElement()
Create a new PileupElement based on the current state of this element Must not be a left or right edge @return a pileup element

Examples of org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine.makePileupElement()

        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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Examples of org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine.makePileupElement()

    @Test(dataProvider = "PrevAndNextTest")
    public void testPrevAndNextTest(final GATKSAMRecord read, final CigarOperator firstOp, final CigarOperator lastOp, final List<CigarOperator> ops) {
        final AlignmentStateMachine state = new AlignmentStateMachine(read);


        state.stepForwardOnGenome();
        final PileupElement pe = state.makePileupElement();
        Assert.assertEquals(pe.getBetweenNextPosition().size(), ops.size());
        Assert.assertEquals(pe.getBetweenPrevPosition().size(), 0);
        assertEqualsOperators(pe.getBetweenNextPosition(), ops);
        Assert.assertEquals(pe.getPreviousOnGenomeCigarElement(), null);
        Assert.assertNotNull(pe.getNextOnGenomeCigarElement());

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Examples of org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine.makePileupElement()

        Assert.assertEquals(pe.getPreviousOnGenomeCigarElement(), null);
        Assert.assertNotNull(pe.getNextOnGenomeCigarElement());
        Assert.assertEquals(pe.getNextOnGenomeCigarElement().getOperator(), lastOp);


        state.stepForwardOnGenome();
        final PileupElement pe2 = state.makePileupElement();
        Assert.assertEquals(pe2.getBetweenPrevPosition().size(), ops.size());
        Assert.assertEquals(pe2.getBetweenNextPosition().size(), 0);
        assertEqualsOperators(pe2.getBetweenPrevPosition(), ops);
        Assert.assertNotNull(pe2.getPreviousOnGenomeCigarElement());
        Assert.assertEquals(pe2.getPreviousOnGenomeCigarElement().getOperator(), firstOp);

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