From 33f6e6d7951d8f5aebdf11f43f0b70741cb4b4bd Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 30 Jan 2015 12:51:56 +0100
Subject: [PATCH] Use AsyncFastqWriter instead of BasicFastqWriter
---
.../scala/nl/lumc/sasc/biopet/tools/FastqSync.scala | 11 ++++++-----
.../nl/lumc/sasc/biopet/tools/FastqSyncTest.scala | 6 +++---
2 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 089efa171..382b59925 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -17,7 +17,7 @@ import scala.collection.JavaConverters._
import argonaut._, Argonaut._
import scalaz._, Scalaz._
-import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
+import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
@@ -185,8 +185,8 @@ object FastqSync extends ToolCommand {
def writeSyncedFastq(sync: Stream[(FastqRecord, FastqRecord)],
counts: SyncCounts,
- outputFastq1: BasicFastqWriter,
- outputFastq2: BasicFastqWriter): Unit = {
+ outputFastq1: AsyncFastqWriter,
+ outputFastq2: AsyncFastqWriter): Unit = {
sync.foreach {
case (rec1, rec2) =>
outputFastq1.write(rec1)
@@ -281,8 +281,9 @@ object FastqSync extends ToolCommand {
new FastqReader(commandArgs.inputFastq2))
writeSyncedFastq(synced, counts,
- new BasicFastqWriter(commandArgs.outputFastq1),
- new BasicFastqWriter(commandArgs.outputFastq2)
+ // using 3000 for queue size to approximate NFS buffer
+ new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq1), 3000),
+ new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq2), 3000)
)
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
index 1c4a02b05..1c98a36f2 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
@@ -8,7 +8,7 @@ import java.io.File
import java.nio.file.Paths
import scala.collection.JavaConverters._
-import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
+import htsjdk.samtools.fastq.{ AsyncFastqWriter, FastqReader, FastqRecord }
import org.mockito.Mockito.{ inOrder => inOrd, when }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
@@ -191,8 +191,8 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
}
@Test def testWriteSynced() = {
- val aMock = mock[BasicFastqWriter]
- val bMock = mock[BasicFastqWriter]
+ val aMock = mock[AsyncFastqWriter]
+ val bMock = mock[AsyncFastqWriter]
val sync = Stream(
(new FastqRecord("1", "A", "", "H"), new FastqRecord("1", "T", "", "E")),
(new FastqRecord("2", "A", "", "H"), new FastqRecord("2", "T", "", "E")))
--
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