From 27db07f0d450c67e35f84bba6d17466c84da5672 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 24 Aug 2015 18:37:12 +0200
Subject: [PATCH] Added auto detect on large indexes for bowtie
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala | 5 +++++
1 file changed, 5 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 9acf9a1dd..088123a76 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
@@ -58,16 +58,21 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
var strata: Boolean = config("strata", default = false)
var maqerr: Option[Int] = config("maqerr")
var maxins: Option[Int] = config("maxins")
+ var largeIndex: Boolean = config("large-index", default = false)
override def beforeGraph() {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
+ val basename = reference.getName.stripSuffix(".fasta").stripSuffix(".fa")
+ if (reference.getParentFile.list().toList.filter(_.startsWith(basename)).exists(_.endsWith(".ebwtl")))
+ largeIndex = config("large-index", default = true)
}
/** return commandline to execute */
def cmdLine = required(executable) +
optional("--threads", threads) +
conditional(sam, "--sam") +
+ conditional(largeIndex, "--large-index") +
conditional(best, "--best") +
conditional(strata, "--strata") +
optional("--sam-RG", sam_RG) +
--
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