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Add back compression in GenotypeStream (unconditional). #1690

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Apr 18, 2017
Merged

Add back compression in GenotypeStream (unconditional). #1690

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11 changes: 7 additions & 4 deletions src/main/scala/is/hail/variant/GenotypeStream.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@ package is.hail.variant
import java.nio.ByteBuffer

import is.hail.expr.{TBinary, TInt, TStruct, Type}
import is.hail.utils._
import is.hail.utils.{ByteIterator, _}
import net.jpountz.lz4.LZ4Factory
import org.apache.spark.sql.Row
import org.apache.spark.sql.types._
import org.apache.spark.sql.types.{StructType, _}

import scala.collection.mutable

Expand Down Expand Up @@ -56,7 +56,7 @@ object LZ4Utils {
compressed.take(compressedLen)
}

def decompress(decompLen: Int, a: Array[Byte]): Array[Byte] = {
def decompress(decompLen: Int, a: Array[Byte]) = {
val decomp = Array.ofDim[Byte](decompLen)
val compLen = decompressor.decompress(a, 0, decomp, 0, decompLen)
assert(compLen == a.length)
Expand Down Expand Up @@ -169,5 +169,8 @@ class GenotypeStreamBuilder(nAlleles: Int, isDosage: Boolean = false)
b.clear()
}

override def result(): GenotypeStream = GenotypeStream(nAlleles, isDosage, None, b.result())
override def result(): GenotypeStream = {
val a = b.result()
GenotypeStream(nAlleles, isDosage, Some(a.length), LZ4Utils.compress(a))
}
}