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CoverageSuite.scala
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CoverageSuite.scala
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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you 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.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.formats.avro.Feature
class CoverageSuite extends ADAMFunSuite {
sparkTest("Convert to coverage from valid Feature") {
// create a valid feature
val featureToConvert =
Feature.newBuilder()
.setContigName("chr1")
.setStart(1)
.setEnd(2)
.setScore(100)
.build()
val coverageAfterConversion = Coverage(featureToConvert)
// all fields should match between the two
assert(coverageAfterConversion.start == featureToConvert.start)
assert(coverageAfterConversion.end == featureToConvert.end)
assert(coverageAfterConversion.contigName == featureToConvert.contigName)
assert(coverageAfterConversion.count == featureToConvert.score)
}
sparkTest("Convert to coverage from valid Feature with name") {
// create a valid feature
val featureToConvert =
Feature.newBuilder()
.setContigName("chr1")
.setStart(1)
.setEnd(2)
.setScore(100)
.setName("coverageName")
.build()
val coverageAfterConversion = Coverage(featureToConvert)
// all fields should match between the two
assert(coverageAfterConversion.start == featureToConvert.start)
assert(coverageAfterConversion.end == featureToConvert.end)
assert(coverageAfterConversion.contigName == featureToConvert.contigName)
assert(coverageAfterConversion.count == featureToConvert.score)
assert(coverageAfterConversion.name == Some(featureToConvert.name))
}
sparkTest("Convert to coverage from Feature with null/empty contigName fails with correct error") {
// feature with empty contigname is not valid when converting to Coverage
val featureWithEmptyContigName =
Feature.newBuilder()
.setContigName("")
.setStart(1)
.setEnd(2)
.setScore(100)
.build()
val caughtWithEmptyContigName =
intercept[IllegalArgumentException](Coverage(featureWithEmptyContigName))
assert(caughtWithEmptyContigName.getMessage == "requirement failed: Features must have Contig name to convert to Coverage")
// feature without contigname is not valid when converting to Coverage
val featureWithNullContigName =
Feature.newBuilder()
.setStart(1)
.setEnd(2)
.setScore(100)
.build()
val caughtWithNullContigName =
intercept[IllegalArgumentException](Coverage(featureWithNullContigName))
assert(caughtWithNullContigName.getMessage == "requirement failed: Features must have Contig name to convert to Coverage")
}
sparkTest("Convert to coverage from Feature with no start/end position fails with correct error") {
// feature without start position is invalid when converting to Coverage
val featureWithoutStartPosition =
Feature.newBuilder()
.setContigName("chr1")
.setEnd(2)
.setScore(100)
.build()
val caughtWithoutStartPosition =
intercept[IllegalArgumentException](Coverage(featureWithoutStartPosition))
assert(caughtWithoutStartPosition.getMessage == "requirement failed: Features must have valid position data to convert to Coverage")
// feature without end position is invalid when converting to Coverage
val featureWithoutEndPosition =
Feature.newBuilder()
.setContigName("chr1")
.setStart(1)
.setScore(100)
.build()
val caughtWithoutEndPosition =
intercept[IllegalArgumentException](Coverage(featureWithoutEndPosition))
assert(caughtWithoutEndPosition.getMessage == "requirement failed: Features must have valid position data to convert to Coverage")
}
sparkTest("Convert to coverage from Feature with no score fails with correct error") {
// feature without score is invalid when converting to Coverage
val featureWithoutScore =
Feature.newBuilder()
.setContigName("chr1")
.setStart(1)
.setEnd(2)
.build()
val caughtWithoutScore =
intercept[IllegalArgumentException](Coverage(featureWithoutScore))
assert(caughtWithoutScore.getMessage == "requirement failed: Features must have valid score to convert to Coverage")
}
}