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Remove uses of VariantContextSetBuilder in all unit tests #819

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Remove uses of VariantContextSetBuilder in all unit tests #819

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2f50599
Remove use of VariantContextSetBuilder from ErrorRateByReadPositionTe…
Mar 28, 2022
9ffb390
Remove VariantContextSetBuilder from ReviewConsensusVariantsTest.scala
Mar 28, 2022
e4da320
Remove VariantContextBuilder from VariantMaskTest.scala
Mar 28, 2022
81e5396
Remove a test that is no longer valid and fix another
Mar 29, 2022
4137b44
Fix one test and remove commented out code
Mar 29, 2022
2a92e69
A few more changes to VariantMaskTest
Mar 30, 2022
9f1b6e7
Fix VariantMask tests
Mar 30, 2022
f0a08f1
Most tests for AssessPhasingTest changed
Mar 30, 2022
ff1578a
Start on next round of changes on AssessPhasingTest
Mar 30, 2022
df69e84
Just one test remaining in AssessPhasingTest
Mar 30, 2022
319887f
Remove some comments in AssessPhasingTest and remove VariantContestSe…
Mar 30, 2022
dd80c2f
Remove some comments, remove VariantContextSetBuilder from MakeTwoSam…
Mar 30, 2022
e0e7db2
Remove VariantContextSetBuilder from JoinVariantContextIteratorTest
Mar 30, 2022
7f63cf1
Remove and import
Mar 30, 2022
c67871d
Remove VariantContextSetBuider from ByIntervalListContextIteratorTest
Mar 30, 2022
e554bdd
Fix UpdateVcfContigNames tests and remove one test in VariantMaskTest
Mar 31, 2022
35a121c
Fixed last few tests for contextsetbuilder
Apr 8, 2022
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14 changes: 7 additions & 7 deletions src/test/scala/com/fulcrumgenomics/bam/ErrorRateByReadPositionTest.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,13 @@
package com.fulcrumgenomics.bam

import java.nio.file.{Files, Path}

import com.fulcrumgenomics.bam.api.SamOrder
import com.fulcrumgenomics.commons.io.PathUtil
import com.fulcrumgenomics.fasta.Converters.ToSAMSequenceDictionary
import com.fulcrumgenomics.fasta.SequenceDictionary
import com.fulcrumgenomics.testing.SamBuilder.{Minus, Plus}
import com.fulcrumgenomics.testing.{ReferenceSetBuilder, SamBuilder, UnitSpec, VariantContextSetBuilder}
import com.fulcrumgenomics.testing.VcfBuilder.Gt
import com.fulcrumgenomics.testing.{ReferenceSetBuilder, SamBuilder, UnitSpec, VcfBuilder}
import com.fulcrumgenomics.util.{Metric, Rscript}
import htsjdk.samtools.util.{Interval, IntervalList}
import com.fulcrumgenomics.util.Metric.Count
Expand Down Expand Up @@ -74,11 +74,11 @@ class ErrorRateByReadPositionTest extends UnitSpec with OptionValues {
private val dict = SequenceDictionary.extract(ref)

private val vcf = {
val builder = new VariantContextSetBuilder().setSequenceDictionary(dict)
builder.addVariant(1, 500, variantAlleles=List("A", "C"), genotypeAlleles=List("A", "C"))
builder.addVariant(2, 500, variantAlleles=List("C", "T"), genotypeAlleles=List("C", "T"))
builder.addVariant(3, 500, variantAlleles=List("G", "A"), genotypeAlleles=List("G", "A"))
builder.addVariant(4, 500, variantAlleles=List("T", "C"), genotypeAlleles=List("T", "C"))
val builder = VcfBuilder(samples=List("sample1"))
builder.add("chr1", 500, alleles=List("A", "C"), gts=Seq(Gt(sample="sample1", gt="0/1")))
builder.add("chr2", 500, alleles=List("C", "T"), gts=Seq(Gt(sample="sample1", gt="0/1")))
builder.add("chr3", 500, alleles=List("G", "A"), gts=Seq(Gt(sample="sample1", gt="0/1")))
builder.add("chr4", 500, alleles=List("T", "C"), gts=Seq(Gt(sample="sample1", gt="0/1")))
builder.toTempFile()
}

Expand Down
34 changes: 23 additions & 11 deletions src/test/scala/com/fulcrumgenomics/umi/ReviewConsensusVariantsTest.scala
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Expand Up @@ -28,9 +28,11 @@ import com.fulcrumgenomics.FgBioDef._
import com.fulcrumgenomics.bam.api.SamOrder
import com.fulcrumgenomics.commons.io.PathUtil
import com.fulcrumgenomics.testing.SamBuilder.{Minus, Plus}
import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec, VariantContextSetBuilder}
import com.fulcrumgenomics.testing.VcfBuilder.Gt
import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec, VcfBuilder}
import com.fulcrumgenomics.umi.ReviewConsensusVariants.ConsensusVariantReviewInfo
import com.fulcrumgenomics.util.{Io, Metric}
import com.fulcrumgenomics.vcf.api._
import htsjdk.samtools.SAMFileHeader
import htsjdk.samtools.reference.{ReferenceSequenceFile, ReferenceSequenceFileFactory}
import htsjdk.samtools.util.IntervalList
Expand Down Expand Up @@ -79,12 +81,19 @@ class ReviewConsensusVariantsTest extends UnitSpec {

lazy val ref: ReferenceSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFasta)

lazy val header = {
lazy val intervalListHeader = {
val h = new SAMFileHeader
h.setSequenceDictionary(ref.getSequenceDictionary)
h
}

lazy val vcfDefaultHeader: VcfHeader = VcfBuilder.DefaultHeader.copy(
contigs = ref.getSequenceDictionary.getSequences.iterator().map { r =>
VcfContigHeader(r.getSequenceIndex, r.getSequenceName, Some(r.getSequenceLength)) } .toIndexedSeq
)

// lazy val vcfHeader = VcfHeader(ref.)

// We're going to simulate raw reads and consensuses as if there were variants at:
// chr1:10
// chr1:20
Expand Down Expand Up @@ -180,7 +189,7 @@ class ReviewConsensusVariantsTest extends UnitSpec {
val rawOut = outBase.getParent.resolve(s"${outBase.getFileName}.grouped.bam")
val txtOut = outBase.getParent.resolve(s"${outBase.getFileName}.txt")
val intervals = makeTempFile("empty.", ".interval_list")
new IntervalList(header).write(intervals.toFile)
new IntervalList(intervalListHeader).write(intervals.toFile)
new ReviewConsensusVariants(input=intervals, consensusBam=consensusBam, groupedBam=rawBam, ref=refFasta, output=outBase).execute()

conOut.toFile.exists() shouldBe true
Expand All @@ -199,9 +208,9 @@ class ReviewConsensusVariantsTest extends UnitSpec {
val txtOut = outBase.getParent.resolve(s"${outBase.getFileName}.txt")
val intervals = makeTempFile("empty.", ".vcf")

val vcfBuilder = VariantContextSetBuilder("s1")
vcfBuilder.header.setSequenceDictionary(header.getSequenceDictionary)
val vcfBuilder = VcfBuilder(vcfDefaultHeader.copy(samples=IndexedSeq("s1")))
vcfBuilder.write(intervals)

new ReviewConsensusVariants(input=intervals, consensusBam=consensusBam, groupedBam=rawBam, ref=refFasta, output=outBase).execute()

conOut.toFile.exists() shouldBe true
Expand All @@ -219,12 +228,15 @@ class ReviewConsensusVariantsTest extends UnitSpec {
val rawOut = outBase.getParent.resolve(s"${outBase.getFileName}.grouped.bam")
val txtOut = outBase.getParent.resolve(s"${outBase.getFileName}.txt")

val vcfBuilder = new VariantContextSetBuilder(sampleNames=List("tumor"))
vcfBuilder.header.setSequenceDictionary(this.header.getSequenceDictionary)
vcfBuilder.addVariant(refIdx=0, start=10, variantAlleles=List("A","T"), genotypeAlleles=List("A","T"), genotypeAttributes=Map("AF" -> 0.01))
vcfBuilder.addVariant(refIdx=0, start=20, variantAlleles=List("A","C"), genotypeAlleles=List("A","C"), genotypeAttributes=Map("AF" -> 0.01))
vcfBuilder.addVariant(refIdx=0, start=30, variantAlleles=List("A","G"), genotypeAlleles=List("A","G"), genotypeAttributes=Map("AF" -> 0.01))
vcfBuilder.addVariant(refIdx=1, start=20, variantAlleles=List("C","T"), genotypeAlleles=List("C","T"), genotypeAttributes=Map("AD" -> Array(100,2)))
val vcfBuilder = VcfBuilder(vcfDefaultHeader.copy(
samples=IndexedSeq("tumor"),
infos = Seq(VcfInfoHeader(id="AF", count=VcfCount.OnePerAllele, kind=VcfFieldType("Float"), description="Allele Frequency"),
VcfInfoHeader(id="AD", count=VcfCount.OnePerAllele, kind=VcfFieldType("Integer"), description="Allele Depth)")))
)
vcfBuilder.add(chrom="chr1", pos=10, alleles=Seq("A", "T"), gts=Seq(Gt(sample="tumor", gt="0/1")),info=Map("AF" -> 0.01))
vcfBuilder.add(chrom="chr1", pos=20, alleles=Seq("A", "C"), gts=Seq(Gt(sample="tumor", gt="0/1")),info=Map("AF" -> 0.01))
vcfBuilder.add(chrom="chr1", pos=30, alleles=Seq("A", "G"), gts=Seq(Gt(sample="tumor", gt="0/1")),info=Map("AF" -> 0.01))
vcfBuilder.add(chrom="chr2", pos=20, alleles=Seq("C", "T"), gts=Seq(Gt(sample="tumor", gt="0/1")),info=Map("AD" -> Seq(100, 2)))

new ReviewConsensusVariants(input=vcfBuilder.toTempFile(), consensusBam=consensusBam, groupedBam=rawBam, ref=refFasta, output=outBase).execute()

Expand Down
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