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fix tests
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@jdidion
jdidion committed Sep 29, 2023
1 parent fbef4b8 commit 4fee506
Showing 1 changed file with 31 additions and 30 deletions.
61 changes: 31 additions & 30 deletions src/test/scala/com/fulcrumgenomics/sv/tools/SvPileupTest.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -47,35 +47,35 @@ class SvPileupTest extends UnitSpec {
// any overlapping segments or jumping backwards between segments is indicative of a breakpoint

// What you might get from a read pair with a gap between the two reads
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=150) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=150, dict=builder.dict) shouldBe false

// same segment but jumping backwards
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=earlier, maxWithinReadDistance=5, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=earlier, maxWithinReadDistance=5, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true

// overlapping segments but still jumping backwards
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=overlap, maxWithinReadDistance=5, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=overlap, maxWithinReadDistance=5, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true

// non-overlapping segments from the same read, testing various values for maxWithinReadDistance
// Note that the inner distance between two blocks is defined as `later.start - earlier.end`, so for
// this case that is 150-100 = 50, so a breakpoint should be called when the maxWithinReadDistance < 50.
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance= 5, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=25, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=48, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=49, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=50, maxBetweenReadDistance=150) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=51, maxBetweenReadDistance=150) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance= 5, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=25, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=48, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=49, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=50, maxBetweenReadDistance=150, dict=builder.dict) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later, maxWithinReadDistance=51, maxBetweenReadDistance=150, dict=builder.dict) shouldBe false

// non-overlapping segments where the later segment is "both" so indicates a split read breakpoint
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance= 5, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=25, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=49, maxBetweenReadDistance=150) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=75, maxBetweenReadDistance=150) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance= 5, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=25, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=49, maxBetweenReadDistance=150, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=Both), maxWithinReadDistance=75, maxBetweenReadDistance=150, dict=builder.dict) shouldBe false

// non-overlapping segments where the later segment is "Read2" so between read distance should be used
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=5 ) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=25) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=49) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=75) shouldBe false
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=5, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=25, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=49, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(seg1=earlier, seg2=later.copy(origin=ReadTwo), maxWithinReadDistance=5, maxBetweenReadDistance=75, dict=builder.dict) shouldBe false
}

"SvPileup.isIntraContigBreakpoint" should "identify when two segments flip strand" in {
Expand All @@ -88,22 +88,22 @@ class SvPileupTest extends UnitSpec {
val r2 = f2.copy(positiveStrand=false)

// Simple tests that should not call breakpoints
SvPileup.isIntraContigBreakpoint(f1, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe false
SvPileup.isIntraContigBreakpoint(r2, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe false
SvPileup.isIntraContigBreakpoint(f1, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe false
SvPileup.isIntraContigBreakpoint(r2, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe false

// Now what if we make them different reads
SvPileup.isIntraContigBreakpoint(f1, f2.copy(origin=ReadTwo), maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe false
SvPileup.isIntraContigBreakpoint(r2, r1.copy(origin=ReadTwo), maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe false
SvPileup.isIntraContigBreakpoint(f1, f2.copy(origin=ReadTwo), maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe false
SvPileup.isIntraContigBreakpoint(r2, r1.copy(origin=ReadTwo), maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe false

// But any combination on different strands should yield a breakpoint
SvPileup.isIntraContigBreakpoint(f1, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(f1, r2, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(f2, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(f2, r2, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(r1, f1, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(r1, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(r2, f1, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(r2, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500) shouldBe true
SvPileup.isIntraContigBreakpoint(f1, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(f1, r2, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(f2, r1, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(f2, r2, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(r1, f1, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(r1, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(r2, f1, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
SvPileup.isIntraContigBreakpoint(r2, f2, maxWithinReadDistance=500, maxBetweenReadDistance=500, dict=builder.dict) shouldBe true
}

//////////////////////////////////////////////////////////////////////////////
Expand Down Expand Up @@ -136,7 +136,8 @@ class SvPileupTest extends UnitSpec {
template = t,
maxWithinReadDistance = 5,
maxReadPairInnerDistance = 1000,
minUniqueBasesToAdd = 10
minUniqueBasesToAdd = 10,
dict = builder.dict
)

/** Short hand for constructing a BreakpointEvidence. */
Expand Down

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