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ReferencePositionSuite.scala
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ReferencePositionSuite.scala
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/**
* Copyright 2014. Regents of the University of California.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.models
import org.scalatest.FunSuite
import org.bdgenomics.adam.avro.{ ADAMContig, ADAMGenotype, ADAMPileup, ADAMRecord, ADAMVariant }
class ReferencePositionSuite extends FunSuite {
test("create reference position from mapped read") {
val contig = ADAMContig.newBuilder
.setContigName("chr1")
.build
val read = ADAMRecord.newBuilder()
.setContig(contig)
.setStart(1L)
.setReadMapped(true)
.build()
val refPosOpt = ReferencePosition(read)
assert(refPosOpt.isDefined)
val refPos = refPosOpt.get
assert(refPos.referenceName === "chr1")
assert(refPos.pos === 1L)
}
test("create reference position from unmapped read") {
val read = ADAMRecord.newBuilder()
.setReadMapped(false)
.build()
val refPosOpt = ReferencePosition(read)
assert(refPosOpt.isEmpty)
}
test("create reference position from mapped read but contig not specified") {
val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setStart(1L)
.build()
val refPosOpt = ReferencePosition(read)
assert(refPosOpt.isEmpty)
}
test("create reference position from mapped read but contig is underspecified") {
val contig = ADAMContig.newBuilder
// contigName is NOT set
//.setContigName("chr1")
.build
val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setStart(1L)
.setContig(contig)
.build()
val refPosOpt = ReferencePosition(read)
assert(refPosOpt.isEmpty)
}
test("create reference position from mapped read but start not specified") {
val contig = ADAMContig.newBuilder
.setContigName("chr1")
.build
val read = ADAMRecord.newBuilder()
.setReadMapped(true)
.setContig(contig)
.build()
val refPosOpt = ReferencePosition(read)
assert(refPosOpt.isEmpty)
}
test("create reference position from pileup") {
val contig = ADAMContig.newBuilder
.setContigName("chr2")
.build
val pileup = ADAMPileup.newBuilder()
.setPosition(2L)
.setContig(contig)
.build()
val refPos = ReferencePosition(pileup)
assert(refPos.referenceName === "chr2")
assert(refPos.pos === 2L)
}
test("create reference position from variant") {
val variant = ADAMVariant.newBuilder()
.setContig(ADAMContig.newBuilder.setContigName("chr10").build())
.setReferenceAllele("A")
.setVariantAllele("T")
.setPosition(10L)
.build()
val refPos = ReferencePosition(variant)
assert(refPos.referenceName === "chr10")
assert(refPos.pos === 10L)
}
test("create reference position from genotype") {
val variant = ADAMVariant.newBuilder()
.setPosition(100L)
.setContig(ADAMContig.newBuilder.setContigName("chr10").build())
.setReferenceAllele("A")
.setVariantAllele("T")
.build()
val genotype = ADAMGenotype.newBuilder()
.setVariant(variant)
.setSampleId("NA12878")
.build()
val refPos = ReferencePosition(genotype)
assert(refPos.referenceName === "chr10")
assert(refPos.pos === 100L)
}
}