From b17079d864d42c73737f771af1397a439ef01cd5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 12:03:59 +0200
Subject: [PATCH] Added samtools sort
---
.../extensions/samtools/SamtoolsSort.scala | 30 +++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
new file mode 100644
index 000000000..d2f723f9e
--- /dev/null
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.extensions.samtools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvanthof on 22/09/15.
+ */
+class SamtoolsSort(val root: Configurable) extends Samtools {
+
+ @Input(required = true)
+ var input: File = _
+
+ @Output
+ var output: File = _
+
+ val compresion: Option[Int] = config("l")
+ val outputFormat: Option[String] = config("O")
+ val sortByName: Boolean = config("sort_by_name", default = false)
+ val prefix: String = config("prefix", default = new File(qSettings.tempDirectory, output.getAbsolutePath))
+
+ def cmdLine = optional("-m", (coreMemeory + "G")) +
+ optional("-@", threads) +
+ optional("-O", outputFormat) +
+ conditional(sortByName, "-n") +
+ (if (outputAsStsout) "" else required("-o", output)) +
+ (if (inputAsStdin) "" else required(input))
+}
--
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