List of stepForwardOnGenome() Examples

Examples of stepForwardOnGenome()

org.broadinstitute.gatk.utils.locusiterator.AlignmentStateMachine.stepForwardOnGenome()
the machine is at the first position on the genome When stepForwardOnGenome() advances off the right edge of the read, the state machine is left in a state such that isRightEdge() returns true and returns null, indicating the the machine cannot advance further. The machine may explode, though this is not contracted, if stepForwardOnGenome() is called after a previous call returned null. @return the operator of the cigar element that machine stopped at, null if we advanced off the end of the read
org.broadinstitute.gatk.utils.locusiterator.LIBS_position.stepForwardOnGenome()
Steps forward on the genome. Returns false when done reading the read, true otherwise.

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

    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());

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


    @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);

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

        assertEqualsOperators(pe.getBetweenNextPosition(), ops);
        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());

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Examples of org.broadinstitute.gatk.utils.locusiterator.LIBS_position.stepForwardOnGenome()

        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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