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non-winnowing
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@jdidion
jdidion committed Apr 3, 2024
1 parent f6052af commit 6eb1762
Showing 1 changed file with 60 additions and 45 deletions.
105 changes: 60 additions & 45 deletions src/test/scala/com/fulcrumgenomics/vcf/DownsampleVcfTest.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -369,66 +369,81 @@ class DownsampleVcfTest extends UnitSpec {
Metric.write(metadata, Seq(Sample(SAMPLE_NAME = sample, BASE_COUNT = 100)))

"DownsampleVcf" should "write a new vcf with downsampled genotypes when provided a vcf" in {
List("proportion", "number", "metadata").foreach(
kind => {
List("proportion", "number", "metadata").foreach(kind => {
List(true, false).foreach(winnow => {
// Construct the input VCF
val outVcf = makeTempFile("out", ".vcf.gz")
val windowSize = if (winnow) { 150 } else { 0 }
kind match {
case "proportion" =>
new DownsampleVcf(input=inVcf,
output=outVcf,
proportion=Some(0.01),
windowSize=150).execute()
windowSize=windowSize).execute()
case "number" =>
new DownsampleVcf(input=inVcf,
output=outVcf,
originalBases=Some(100),
downsampleToBases=Some(1),
windowSize=150).execute()
windowSize=windowSize).execute()
case "metadata" =>
new DownsampleVcf(input=inVcf,
output=outVcf,
metadata=Some(metadata),
downsampleToBases=Some(1),
windowSize=150).execute()
windowSize=windowSize).execute()
}

val vs = readVcfRecs(outVcf)
vs should have length 5
val expectedLength = if (winnow) { 5 } else { 6 }
vs should have length expectedLength

val ad0 = vs(0).genotypes("test1")[IndexedSeq[Int]]("AD")
ad0(0) < 110 shouldBe true;
ad0(0) < 110 shouldBe true
ad0(1) < 110 shouldBe true
val pl0 = vs(0).genotypes("test1")[IndexedSeq[Int]]("PL")
pl0(1) shouldBe 0

val offset = if (winnow) {
0
} else {
val ad1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("AD")
ad1(0) shouldBe 8
ad1(1) < 110 shouldBe true
val pl1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("PL")
pl1(2) shouldBe 160
1
}

val ad1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("AD")
ad1(0) shouldBe 0;
ad1(1) < 110 shouldBe true
val pl1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("PL")
pl1(2) shouldBe 0

val ad2 = vs(2).genotypes("test1")[IndexedSeq[Int]]("AD")
ad2(0) < 30 shouldBe true;
val ad2 = vs(1 + offset).genotypes("test1")[IndexedSeq[Int]]("AD")
ad2(0) shouldBe 0
ad2(1) < 110 shouldBe true
val pl2 = vs(2).genotypes("test1")[IndexedSeq[Int]]("PL")
val pl2 = vs(1 + offset).genotypes("test1")[IndexedSeq[Int]]("PL")
pl2(2) shouldBe 0

val ad3 = vs(3).genotypes("test1")[IndexedSeq[Int]]("AD")
ad3(0) < 110 shouldBe true;
ad3(1) shouldBe 0;
val pl3 = vs(3).genotypes("test1")[IndexedSeq[Int]]("PL")
pl3(0) shouldBe 0
val ad3 = vs(2 + offset).genotypes("test1")[IndexedSeq[Int]]("AD")
ad3(0) < 30 shouldBe true
ad3(1) < 110 shouldBe true
val pl3 = vs(2 + offset).genotypes("test1")[IndexedSeq[Int]]("PL")
pl3(2) shouldBe 0

val ad4 = vs(4).genotypes("test1")[IndexedSeq[Int]]("AD")
ad4(0) < 100 shouldBe true;
ad4(1) < 100 shouldBe true;
ad4(0) > 1 shouldBe true;
ad4(1) > 2 shouldBe true;
val pl4 = vs(4).genotypes("test1")[IndexedSeq[Int]]("PL")
pl4(1) shouldBe 0
}
)
val ad4 = vs(3 + offset).genotypes("test1")[IndexedSeq[Int]]("AD")
ad4(0) < 110 shouldBe true
// changes due to random number generator
val expectedAD41 = if (winnow) { 0 } else { 1 }
ad4(1) shouldBe expectedAD41
val pl4 = vs(3 + offset).genotypes("test1")[IndexedSeq[Int]]("PL")
pl4(0) shouldBe 0

val ad5 = vs(4 + offset).genotypes("test1")[IndexedSeq[Int]]("AD")
ad5(0) < 100 shouldBe true
ad5(1) < 100 shouldBe true
ad5(0) > 1 shouldBe true
ad5(1) > 2 shouldBe true
val pl5 = vs(4 + offset).genotypes("test1")[IndexedSeq[Int]]("PL")
pl5(1) shouldBe 0
})
})

}

Expand Down Expand Up @@ -465,50 +480,50 @@ class DownsampleVcfTest extends UnitSpec {
vs should have length 7

val ad0 = vs(0).genotypes("test1")[IndexedSeq[Int]]("AD")
ad0(0) < 110 shouldBe true;
ad0(0) < 110 shouldBe true
ad0(1) < 110 shouldBe true
val pl0 = vs(0).genotypes("test1")[IndexedSeq[Int]]("PL")
pl0(1) shouldBe 0

val ad1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("AD")
ad1(0) shouldBe 0;
ad1(0) shouldBe 0
ad1(1) < 110 shouldBe true
val pl1 = vs(1).genotypes("test1")[IndexedSeq[Int]]("PL")
pl1(2) shouldBe 0

val ad2 = vs(2).genotypes("test1")[IndexedSeq[Int]]("AD")
ad2(0) shouldBe 0;
ad2(0) shouldBe 0
ad2(1) shouldBe 0
val pl2 = vs(2).genotypes("test1")[IndexedSeq[Int]]("PL")
pl2(0) shouldBe 0;
pl2(1) shouldBe 0;
pl2(0) shouldBe 0
pl2(1) shouldBe 0
pl2(2) shouldBe 0

val ad3 = vs(3).genotypes("test1")[IndexedSeq[Int]]("AD")
ad3(0) < 30 shouldBe true;
ad3(0) < 30 shouldBe true
ad3(1) < 110 shouldBe true
val pl3 = vs(3).genotypes("test1")[IndexedSeq[Int]]("PL")
pl3(2) shouldBe 0

val ad4 = vs(4).genotypes("test1")[IndexedSeq[Int]]("AD")
ad4(0) < 110 shouldBe true;
ad4(1) shouldBe 0;
ad4(0) < 110 shouldBe true
ad4(1) shouldBe 0
val pl4 = vs(4).genotypes("test1")[IndexedSeq[Int]]("PL")
pl4(0) shouldBe 0

val ad5 = vs(5).genotypes("test1")[IndexedSeq[Int]]("AD")
ad5(0) shouldBe 0;
ad5(0) shouldBe 0
ad5(1) shouldBe 0
val pl5 = vs(5).genotypes("test1")[IndexedSeq[Int]]("PL")
pl5(0) shouldBe 0;
pl5(1) shouldBe 0;
pl5(0) shouldBe 0
pl5(1) shouldBe 0
pl5(2) shouldBe 0

val ad6 = vs(6).genotypes("test1")[IndexedSeq[Int]]("AD")
ad6(0) < 100 shouldBe true;
ad6(1) < 100 shouldBe true;
ad6(0) > 1 shouldBe true;
ad6(1) > 2 shouldBe true;
ad6(0) < 100 shouldBe true
ad6(1) < 100 shouldBe true
ad6(0) > 1 shouldBe true
ad6(1) > 2 shouldBe true
val pl6 = vs(6).genotypes("test1")[IndexedSeq[Int]]("PL")
pl6(1) shouldBe 0
}
Expand Down

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