From 1cc49dfc4c4c50629b4655435a7d56b27beca7d5 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 28 Jul 2014 17:58:37 +0200
Subject: [PATCH] Update Seqtk wrapper namespace
---
.../sasc/biopet/function/seqtk/Seqtk.scala | 21 +++++++++++++++++++
.../{Seqtk.scala => seqtk/SeqtkSeq.scala} | 11 +---------
2 files changed, 22 insertions(+), 10 deletions(-)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/Seqtk.scala
rename biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/{Seqtk.scala => seqtk/SeqtkSeq.scala} (90%)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/Seqtk.scala
new file mode 100644
index 000000000..3d83d397d
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/Seqtk.scala
@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author Wibowo Arindrarto
+ */
+
+package nl.lumc.sasc.biopet.function.seqtk
+
+import java.io.File
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+/**
+ * Abstract class for all seqtk wrappers.
+ */
+abstract class Seqtk extends BiopetCommandLineFunction {
+ executable = config("exe", default = "seqtk", submodule = "seqtk")
+ override def versionCommand = executable
+ override val versionRegex = """Version: (.*)""".r
+}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/SeqtkSeq.scala
similarity index 90%
rename from biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
rename to biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/SeqtkSeq.scala
index 286b7235b..eb592a44b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/SeqtkSeq.scala
@@ -4,22 +4,13 @@
* @author Wibowo Arindrarto
*/
-package nl.lumc.sasc.biopet.function
+package nl.lumc.sasc.biopet.function.seqtk
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
-/**
- * Abstract class for all seqtk wrappers.
- */
-abstract class Seqtk extends BiopetCommandLineFunction {
- executable = config("exe", default = "seqtk", submodule = "seqtk")
- override def versionCommand = executable
- override val versionRegex = """Version: (.*)""".r
-}
-
/**
* Wrapper for the seqtk seq subcommand.
* Written based on seqtk version 1.0-r63-dirty.
--
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