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

Example 16 with BreakendSummary

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

the class TruthAnnotatorTest method match_should_match_both_breakpoint_breakends.

@Test
public void match_should_match_both_breakpoint_breakends() {
    assertTrue(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, FWD, 1), new BreakendSummary(0, BWD, 10)), new BreakpointSummary(new BreakendSummary(0, FWD, 1), new BreakendSummary(0, BWD, 10)), 0, 0));
    assertTrue(TruthAnnotator.matches(new BreakpointSummary(new BreakendSummary(0, BWD, 10), new BreakendSummary(0, FWD, 1)), new BreakpointSummary(new BreakendSummary(0, FWD, 1), new BreakendSummary(0, BWD, 10)), 0, 0));
}

Example 17 with BreakendSummary

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

the class ModelsTest method calculateBreakend_should_reduce_to_consistent_set.

@Test
public void calculateBreakend_should_reduce_to_consistent_set() {
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedEvidence(new BreakendSummary(0, FWD, 10, 10, 15)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 12, 12, 18))));
    assertEquals(new BreakendSummary(0, FWD, 13, 12, 15), bs);
}

Example 18 with BreakendSummary

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

the class ModelsTest method calculateBreakend_should_infer_direction_from_support.

@Test
public void calculateBreakend_should_infer_direction_from_support() {
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedEvidence(new BreakendSummary(0, FWD, 10, 10, 15)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 10, 10, 16)), new MockDirectedEvidence(new BreakendSummary(0, BWD, 12, 12, 18))));
    assertEquals(new BreakendSummary(0, FWD, 12, 10, 15), bs);
}

Example 19 with BreakendSummary

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

the class ModelsTest method calculateBreakend_calculate_interval_with_greatest_support.

@Test
public void calculateBreakend_calculate_interval_with_greatest_support() {
    // 1         2
    // 12345678901234567890123456789
    // ****** **@@
    // ****@@@
    // *******
    // ^
    // most support
    BreakendSummary bs = Models.calculateBreakend(getContext().getLinear(), Lists.newArrayList(new MockDirectedEvidence(new BreakendSummary(0, FWD, 10, 10, 15)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 18, 15, 18)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 17, 17, 18)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 15, 9, 15)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 20, 19, 20)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 21, 19, 21))));
    assertEquals(new BreakendSummary(0, FWD, 15, 15, 15), bs);
}