From d526426fba3fe6caff09bc8901432a14b010da29 Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 9 Apr 2015 11:56:44 +0200
Subject: [PATCH] added extra options to bowtie
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala | 2 ++
1 file changed, 2 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index ac30b3b32..ec95ce3c5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -57,6 +57,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var maxbts: Option[Int] = config("maxbts")
var strata: Boolean = config("strata", default = false)
var maqerr: Option[Int] = config("maqerr")
+ var maxins: Option[Int] = config("maxins")
/** return commandline to execute */
def cmdLine = {
@@ -72,6 +73,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
optional("-m", m) +
optional("--maxbts", maxbts) +
optional("--maqerr", maqerr) +
+ optional("--maxins", maxins) +
required(reference) +
(R2 match {
case Some(r2) => {
--
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