Examples with BreakpointSummary au.edu.wehi.idsv.BreakpointSummary used on opensource projects

Example 6 with BreakpointSummary

use of au.edu.wehi.idsv.BreakpointSummary in project gridss by PapenfussLab.

the class TruthAnnotatorTest method match_allow_any_interval_overlap.

@Test
public void match_allow_any_interval_overlap() {
    assertTrue(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, FWD, 1, 1, 10), new BreakendSummary(0, BWD, 50, 50, 60)), new BreakpointSummary(new BreakendSummary(0, FWD, 5), new BreakendSummary(0, BWD, 70, 40, 70)), 0, 0));
    assertTrue(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, FWD, 10), new BreakendSummary(0, BWD, 60, 50, 60)), new BreakpointSummary(new BreakendSummary(0, FWD, 10, 10, 11), new BreakendSummary(0, BWD, 40, 40, 50)), 0, 0));
}

Example 7 with BreakpointSummary

use of au.edu.wehi.idsv.BreakpointSummary in project gridss by PapenfussLab.

the class TruthAnnotatorTest method match_should_limit_breakend_reference_homology_matching_to_16bp.

@Test
public void match_should_limit_breakend_reference_homology_matching_to_16bp() {
    assertTrue(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, FWD, 1), new BreakendSummary(0, BWD, 1000)), new BreakendSummary(0, FWD, 17), 17, 1));
    assertFalse(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, FWD, 1), new BreakendSummary(0, BWD, 1000)), new BreakendSummary(0, FWD, 18), 17, 0));
}

Example 8 with BreakpointSummary

use of au.edu.wehi.idsv.BreakpointSummary in project gridss by PapenfussLab.

the class ModelsTest method calculateBreakend_should_return_overlap_for_multiple_evidence.

@Test
public void calculateBreakend_should_return_overlap_for_multiple_evidence() {
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedBreakpoint(new BreakpointSummary(0, FWD, 1, 1, 4, 1, BWD, 2, 2, 2)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 3, 3, 5))));
    assertEquals(new BreakendSummary(0, FWD, 3, 3, 4), bs);
}

Example 9 with BreakpointSummary

use of au.edu.wehi.idsv.BreakpointSummary in project gridss by PapenfussLab.

the class ModelsTest method calculateBreakend_should_return_breakend.

@Test
public void calculateBreakend_should_return_breakend() {
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedBreakpoint(new BreakpointSummary(0, FWD, 1, 1, 2, 1, BWD, 2, 2, 2))));
    assertEquals(new BreakendSummary(0, FWD, 1, 1, 2), bs);
    assertEquals(BreakendSummary.class, bs.getClass());
}

Example 10 with BreakpointSummary

use of au.edu.wehi.idsv.BreakpointSummary in project gridss by PapenfussLab.

the class ModelsTest method calculateBreakend_should_return_interval_for_single_evidence.

@Test
public void calculateBreakend_should_return_interval_for_single_evidence() {
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedBreakpoint(new BreakpointSummary(0, FWD, 1, 1, 2, 1, BWD, 2, 2, 2))));
    assertEquals(new BreakendSummary(0, FWD, 1, 1, 2), bs);
}