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TransformGenotypesSuite.scala
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TransformGenotypesSuite.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.cli
import org.bdgenomics.adam.ds.ADAMContext._
import org.bdgenomics.adam.util.ADAMFunSuite
class TransformGenotypesSuite extends ADAMFunSuite {
sparkTest("save a file sorted by contig index") {
val inputPath = copyResource("random.vcf")
val intermediatePath = tmpFile("genotypes.adam")
val actualPath = tmpFile("sorted.vcf")
val expectedPath = testFile("sorted.vcf")
TransformGenotypes(
Array(inputPath, intermediatePath)
).run(sc)
TransformGenotypes(
Array(intermediatePath, actualPath, "-sort_on_save", "-single")
).run(sc)
checkFiles(expectedPath, actualPath)
}
sparkTest("save a lexicographically sorted file") {
val inputPath = copyResource("random.vcf")
val intermediatePath = tmpFile("genotypes.lex.adam")
val actualPath = tmpFile("sorted.lex.vcf")
val expectedPath = testFile("sorted.lex.vcf")
TransformGenotypes(
Array(inputPath, intermediatePath)
).run(sc)
TransformGenotypes(
Array(intermediatePath, actualPath, "-sort_lexicographically_on_save", "-single")
).run(sc)
checkFiles(expectedPath, actualPath)
}
sparkTest("transform VCF without nested annotations") {
val inputPath = copyResource("random.vcf")
val intermediatePath = tmpFile("genotypes.adam")
TransformGenotypes(
Array(inputPath, intermediatePath)
).run(sc)
val genotypes = sc.loadGenotypes(intermediatePath)
val genotype = genotypes.sort().rdd.first()
assert(genotype.getVariant().getAnnotation() == null)
}
sparkTest("transform VCF with nested annotations") {
val inputPath = copyResource("random.vcf")
val intermediatePath = tmpFile("genotypes.nested-annotations.adam")
TransformGenotypes(
Array(inputPath, intermediatePath, "-nested_annotations")
).run(sc)
val genotypes = sc.loadGenotypes(intermediatePath)
val genotype = genotypes.sort().rdd.first()
assert(genotype.getVariant().getAnnotation() != null)
assert(genotype.getVariant().getAnnotation().get("alleleCount") === 2)
}
}