From 43c985ef90e1368e6868a590c5c7ad0f3b6f5666 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 4 Aug 2014 11:28:12 +0200
Subject: [PATCH] Added SeqtkSeq function to Flexiprep
---
.../sasc/biopet/extensions/seqtk/Seqtk.scala | 2 +-
.../biopet/extensions/seqtk/SeqtkSeq.scala | 2 +-
.../biopet/pipelines/flexiprep/SeqtkSeq.scala | 38 +++++++++++++++++++
3 files changed, 40 insertions(+), 2 deletions(-)
create mode 100644 flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
index 8684c7a0c..6fbc166ab 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
@@ -4,7 +4,7 @@
* @author Wibowo Arindrarto
*/
-package nl.lumc.sasc.biopet.function.seqtk
+package nl.lumc.sasc.biopet.extensions.seqtk
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
index 1bd2426a0..ef908ea13 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
@@ -4,7 +4,7 @@
* @author Wibowo Arindrarto
*/
-package nl.lumc.sasc.biopet.function.seqtk
+package nl.lumc.sasc.biopet.extensions.seqtk
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
new file mode 100644
index 000000000..4d70cd4da
--- /dev/null
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -0,0 +1,38 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.Ln
+
+class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
+ var fastqc: Fastqc = _
+
+ override def beforeCmd {
+ super.beforeCmd
+ if (fastqc != null && Q == None) {
+ Q = fastqc.getEncoding match {
+ case null => None
+ case s if (s.contains("Sanger / Illumina 1.9")) => None
+ case s if (s.contains("Illumina <1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.5")) => Option(64)
+ }
+ if (Q != None) V = true
+ }
+ }
+
+ override def cmdLine = {
+ if (Q != None) {
+ analysisName = getClass.getName
+ super.cmdLine
+ } else {
+ analysisName = getClass.getSimpleName + "-ln"
+ Ln(this, input, output).cmd
+ }
+ }
+}
--
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