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[ADAM-1190] Manually (un)pack IndelRealignmentTarget set. #1191

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merged 1 commit into from Oct 3, 2016
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[ADAM-1190] Manually (un)pack IndelRealignmentTarget set. #1191

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15 changes: 12 additions & 3 deletions ...core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
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Expand Up @@ -198,13 +198,22 @@ class IndelRealignmentTarget(

class TargetSetSerializer extends Serializer[TargetSet] {

val irts = new IndelRealignmentTargetSerializer()

def write(kryo: Kryo, output: Output, obj: TargetSet) = {
kryo.writeClassAndObject(output, obj.set.toList)
output.writeInt(obj.set.size)
obj.set.foreach(innerObj => {
irts.write(kryo, output, innerObj)
})
}

def read(kryo: Kryo, input: Input, klazz: Class[TargetSet]): TargetSet = {
new TargetSet(new TreeSet()(TargetOrdering)
.union(kryo.readClassAndObject(input).asInstanceOf[List[IndelRealignmentTarget]].toSet))
val size = input.readInt()
val array = new Array[IndelRealignmentTarget](size)
(0 until size).foreach(i => {
array(i) = irts.read(kryo, input, classOf[IndelRealignmentTarget])
})
new TargetSet(TreeSet(array: _*)(TargetOrdering))
}
}

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