From 7930bcb4808e675ca35483b827783266570058ed Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 27 Oct 2014 17:10:00 +0100
Subject: [PATCH] Add functions to main
---
.../lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 12 ++++++++++++
1 file changed, 12 insertions(+)
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 98f0c704c..d53b1afd0 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
@@ -223,5 +223,17 @@ object ExtractAlignedFastq extends ToolCommand {
val commandArgs: Args = new OptParser()
.parse(args, Args())
.getOrElse(sys.exit(1))
+
+ val memFunc = makeMembershipFunction(
+ iv = makeFeatureFromString(commandArgs.intervals),
+ inAln = commandArgs.inputBam,
+ minMapQ = commandArgs.minMapQ,
+ commonSuffixLength = commandArgs.commonSuffixLength)
+
+ selectFastqReads(memFunc,
+ inputFastq1 = commandArgs.inputFastq1,
+ inputFastq2 = commandArgs.inputFastq2,
+ outputFastq1 = commandArgs.outputFastq1,
+ outputFastq2 = commandArgs.outputFastq2)
}
}
--
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