From d2e68c8976b2d9b141e8f8480a1f067fce8622b1 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 14 Mar 2016 09:13:29 +0100
Subject: [PATCH] Fix bug when bowtie2 is not able to find reference files
ending with .bt2l (new large file definition)
---
.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
index 793fd7d15..60a690f7c 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
@@ -135,7 +135,12 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
val indexDir = new File(bowtieIndex).getParentFile
val basename = bowtieIndex.stripPrefix(indexDir.getPath + File.separator)
if (indexDir.exists()) {
- if (!indexDir.list().toList.filter(_.startsWith(basename)).exists(_.endsWith(".bt2")))
+ if (!indexDir.list()
+ .toList
+ .filter(_.startsWith(basename))
+ .exists({ p =>
+ p.endsWith(".bt2") || p.endsWith(".bt2l")
+ }))
Logging.addError(s"No index files found for bowtie2 in: $indexDir with basename: $basename")
}
}
--
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