From 717bf892a1bd0abf453d6e31acd6fac534bcfbcf Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 27 Oct 2014 23:49:57 +0100
Subject: [PATCH] Update write function to accept FASTQ readers and writers
---
.../biopet/tools/ExtractAlignedFastq.scala | 26 +++++++++----------
1 file changed, 13 insertions(+), 13 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 72cf7be79..cdbc13e99 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -124,28 +124,28 @@ object ExtractAlignedFastq extends ToolCommand {
}
def selectFastqReads(memFunc: FastqPair => Boolean,
- inputFastq1: File,
- outputFastq1: File,
- inputFastq2: File = null,
- outputFastq2: File = null): Unit = {
+ inputFastq1: FastqReader,
+ outputFastq1: BasicFastqWriter,
+ inputFastq2: FastqReader = null,
+ outputFastq2: BasicFastqWriter = null): Unit = {
- val i1 = new FastqReader(inputFastq1).iterator.asScala
- val o1 = new BasicFastqWriter(outputFastq1)
+ val i1 = inputFastq1.iterator.asScala
val i2 = inputFastq2 match {
case null => Iterator.continually(null)
- case otherwise => new FastqReader(otherwise).iterator.asScala
+ case otherwise => otherwise.iterator.asScala
}
+ val o1 = outputFastq1
val o2 = (inputFastq2, outputFastq2) match {
case (null, null) => null
case (_, null) => throw new IllegalArgumentException("Missing output FASTQ 2")
case (null, _) => throw new IllegalArgumentException("Output FASTQ 2 supplied but there is no input FASTQ 2")
- case (x, y) => new BasicFastqWriter(outputFastq2)
+ case (x, y) => outputFastq2
}
logger.info("Writing output file(s) ...")
// zip, filter based on function, and write to output file(s)
i1.zip(i2)
- .filter((rec) => memFunc(rec._1, rec._2))
+ .filter(rec => memFunc(rec._1, rec._2))
.foreach {
case (rec1, null) =>
o1.write(rec1)
@@ -235,9 +235,9 @@ object ExtractAlignedFastq extends ToolCommand {
commonSuffixLength = commandArgs.commonSuffixLength)
selectFastqReads(memFunc,
- inputFastq1 = commandArgs.inputFastq1,
- inputFastq2 = commandArgs.inputFastq2,
- outputFastq1 = commandArgs.outputFastq1,
- outputFastq2 = commandArgs.outputFastq2)
+ inputFastq1 = new FastqReader(commandArgs.inputFastq1),
+ inputFastq2 = new FastqReader(commandArgs.inputFastq2),
+ outputFastq1 = new BasicFastqWriter(commandArgs.outputFastq1),
+ outputFastq2 = new BasicFastqWriter(commandArgs.outputFastq2))
}
}
--
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