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

Example 1 with MockDirectedEvidence

use of au.edu.wehi.idsv.MockDirectedEvidence 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 2 with MockDirectedEvidence

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

the class ModelsTest method calculateBreakend_should_ignore_overlaps_resulting_in_no_breakend.

@Test
public void calculateBreakend_should_ignore_overlaps_resulting_in_no_breakend() {
    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)), new MockDirectedEvidence(new BreakendSummary(0, FWD, 5, 5, 5))));
    assertEquals(new BreakendSummary(0, FWD, 3, 3, 4), bs);
}

Example 3 with MockDirectedEvidence

use of au.edu.wehi.idsv.MockDirectedEvidence 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 4 with MockDirectedEvidence

use of au.edu.wehi.idsv.MockDirectedEvidence 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 5 with MockDirectedEvidence

use of au.edu.wehi.idsv.MockDirectedEvidence 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);
}