/
IndelTableSuite.scala
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/
IndelTableSuite.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.SparkFunSuite
import org.bdgenomics.formats.avro.{ Contig, Variant }
class IndelTableSuite extends SparkFunSuite {
// indel table containing a 1 bp deletion at chr1, pos 1000
val indelTable = new IndelTable(Map("1" -> Iterable(Consensus("", ReferenceRegion("1", 1000L, 1002L)))))
test("check for indels in a region with known indels") {
assert(indelTable.getIndelsInRegion(ReferenceRegion("1", 0L, 2000L)).length === 1)
}
test("check for indels in a contig that doesn't exist") {
assert(indelTable.getIndelsInRegion(ReferenceRegion("0", 0L, 1L)).length === 0)
}
test("check for indels in a region without known indels") {
assert(indelTable.getIndelsInRegion(ReferenceRegion("1", 1002L, 1005L)).length === 0)
}
sparkTest("build indel table from rdd of variants") {
val ctg1 = Contig.newBuilder()
.setContigName("1")
.build()
val ctg2 = Contig.newBuilder()
.setContigName("2")
.build()
val ins = Variant.newBuilder()
.setContig(ctg1)
.setStart(1000L)
.setReferenceAllele("A")
.setAlternateAllele("ATT")
.build()
val del = Variant.newBuilder()
.setContig(ctg2)
.setStart(50L)
.setReferenceAllele("ACAT")
.setAlternateAllele("A")
.build()
val rdd = sc.parallelize(Seq(ins, del))
val table = IndelTable(rdd)
// check insert
val insT = table.getIndelsInRegion(ReferenceRegion("1", 1000L, 1010L))
assert(insT.length === 1)
assert(insT.head.consensus === "TT")
assert(insT.head.index.referenceName === "1")
assert(insT.head.index.start === 1001)
assert(insT.head.index.end === 1002)
// check delete
val delT = table.getIndelsInRegion(ReferenceRegion("2", 40L, 60L))
assert(delT.length === 1)
assert(delT.head.consensus === "")
assert(delT.head.index.referenceName === "2")
assert(delT.head.index.start === 51)
assert(delT.head.index.end === 54)
}
}