/
LociSetSuite.scala
182 lines (160 loc) · 6.33 KB
/
LociSetSuite.scala
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package org.hammerlab.genomics.loci.set
import org.hammerlab.genomics.loci.parsing.ParsedLoci
import org.hammerlab.genomics.loci.set.test.LociSetUtil
import org.hammerlab.genomics.reference.test.{ ClearContigNames, ContigLengthsUtil, LenientContigNameConversions }
import org.hammerlab.genomics.reference.test.LociConversions._
import org.hammerlab.genomics.reference.{ ContigLengths, ContigName, Locus, NumLoci, PermissiveRegistrar }
import org.hammerlab.spark.test.suite.KryoSparkSuite
import scala.collection.mutable
class LociSetSuite
extends KryoSparkSuite(classOf[Registrar])
with LociSetUtil
with LenientContigNameConversions
with ClearContigNames
with ContigLengthsUtil {
// "loci set invariants" collects some LociSets
register(
classOf[mutable.WrappedArray.ofRef[_]],
PermissiveRegistrar
)
def makeLociSet(str: String, lengths: (ContigName, NumLoci)*): LociSet =
LociSet(ParsedLoci(str), lengths.toMap)
test("properties of empty LociSet") {
val empty = LociSet()
empty.contigs should have size 0
empty.count should ===(0)
empty should ===(lociSet(""))
val empty2 = lociSet("empty1:30-30,empty2:40-40")
empty should ===(empty2)
}
test("count, containment, intersection testing of a loci set") {
val set = lociSet("chr21:100-200,chr20:0-10,chr20:8-15,chr20:100-120,empty:10-10")
set.contigs.map(_.name) should ===(Seq("chr20", "chr21"))
set.count should ===(135)
set("chr20").contains(110) should ===(true)
set("chr20").contains(100) should ===(true)
set("chr20").contains(99) should ===(false)
set("chr20").contains(120) should ===(false)
set("chr20").contains(119) should ===(true)
set("chr20").count should ===(35)
set("chr20").intersects(0, 5) should ===(true)
set("chr20").intersects(0, 1) should ===(true)
set("chr20").intersects(0, 0) should ===(false)
set("chr20").intersects(7, 8) should ===(true)
set("chr20").intersects(9, 11) should ===(true)
set("chr20").intersects(11, 18) should ===(true)
set("chr20").intersects(18, 19) should ===(false)
set("chr20").intersects(14, 80) should ===(true)
set("chr20").intersects(15, 80) should ===(false)
set("chr20").intersects(120, 130) should ===(false)
set("chr20").intersects(119, 130) should ===(true)
set("chr21").contains(99) should ===(false)
set("chr21").contains(100) should ===(true)
set("chr21").contains(200) should ===(false)
set("chr21").count should ===(100)
set("chr21").intersects(110, 120) should ===(true)
set("chr21").intersects(90, 120) should ===(true)
set("chr21").intersects(150, 200) should ===(true)
set("chr21").intersects(150, 210) should ===(true)
set("chr21").intersects(200, 210) should ===(false)
set("chr21").intersects(201, 210) should ===(false)
set("chr21").intersects(90, 100) should ===(false)
set("chr21").intersects(90, 101) should ===(true)
set("chr21").intersects(90, 95) should ===(false)
set("chr21").iterator.toSeq should ===(100 until 200)
}
test("single loci parsing") {
val set = lociSet("chr1:10000")
set.count should ===(1)
set("chr1").contains( 9999) should ===(false)
set("chr1").contains(10000) should ===(true)
set("chr1").contains(10001) should ===(false)
}
test("loci set invariants") {
val sets =
List(
"",
"empty:20-20,empty2:30-30",
"20:100-200",
"with_dots.and_underscores..2:100-200",
"21:300-400",
"X:5-17,X:19-22,Y:50-60",
"chr21:100-200,chr20:0-10,chr20:8-15,chr20:100-120"
)
.map(lociSet)
def checkInvariants(set: LociSet): Unit = {
set should not be null
set.toString should not be null
withClue("invariants for: '%s'".format(set.toString)) {
lociSet(set.toString) should ===(set)
lociSet(set.toString).toString should ===(set.toString)
set should ===(set)
// Test serialization. We hit all sorts of null pointer exceptions here at one point, so we are paranoid about
// checking every pointer.
val parallelized = sc.parallelize(List(set))
val collected = parallelized.collect()
val result = collected(0)
result should ===(set)
}
}
sets.foreach(checkInvariants)
}
test("loci set parsing with contig lengths") {
makeLociSet(
"chr1,chr2,17,chr2:3-5,chr20:10-20",
"chr1" -> 10,
"chr2" -> 20,
"17" -> 12,
"chr20" -> 5000
)
.toString should ===("chr1:0-10,chr2:0-20,17:0-12,chr20:10-20")
}
test("parse half-open interval") {
makeLociSet("chr1:10000-", "chr1" -> 20000).toString should ===("chr1:10000-20000")
}
test("loci set single contig iterator basic") {
val set = lociSet("chr1:20-25,chr1:15-17,chr1:40-43,chr1:40-42,chr1:5-5,chr2:5-6,chr2:6-7,chr2:2-4")
set("chr1").iterator.toSeq should ===(Seq(15, 16, 20, 21, 22, 23, 24, 40, 41, 42))
set("chr2").iterator.toSeq should ===(Seq(2, 3, 5, 6))
val iter1 = set("chr1").iterator
iter1.hasNext should ===(true)
iter1.head should ===(15)
iter1.next() should ===(15)
iter1.head should ===(16)
iter1.next() should ===(16)
iter1.head should ===(20)
iter1.next() should ===(20)
iter1.head should ===(21)
iter1.skipTo(23)
iter1.next() should ===(23)
iter1.head should ===(24)
iter1.skipTo(38)
iter1.head should ===(40)
iter1.hasNext should ===(true)
iter1.skipTo(100)
iter1.hasNext should ===(false)
}
test("loci set single contig iterator: test that skipTo implemented efficiently.") {
val set = lociSet("chr1:2-3,chr1:10-15,chr1:100-100000000000")
val iter1 = set("chr1").iterator
iter1.hasNext should ===(true)
iter1.head should ===(2)
iter1.next() should ===(2)
iter1.next() should ===(10)
iter1.next() should ===(11)
val sixBillion = Locus(6000000000L)
iter1.skipTo(sixBillion) // will hang if it steps through each locus.
iter1.next() should ===(sixBillion)
iter1.next() should ===(sixBillion.next)
iter1.hasNext should ===(true)
val hundredBillion = Locus(100000000000L)
val iter2 = set("chr1").iterator
iter2.skipTo(hundredBillion)
iter2.hasNext should ===(false)
val iter3 = set("chr1").iterator
iter3.skipTo(hundredBillion.prev)
iter3.hasNext should ===(true)
iter3.next() should ===(100000000000L - 1)
iter3.hasNext should ===(false)
}
}