From 8ab8f962732930268104b7ad504603534edb4a55 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 May 2016 08:31:03 +0200
Subject: [PATCH] fix some code warnings
---
.../nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
index af762ed2d..c97fe218f 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
@@ -94,7 +94,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
def commandLine = cmds.mkString(" && ")
}
- if (fastaUris.length > 1 || fastaFiles.filter(_.getName.endsWith(".gz")).nonEmpty) {
+ if (fastaUris.length > 1 || fastaFiles.exists(_.getName.endsWith(".gz"))) {
fastaFiles.foreach { file =>
if (file.getName.endsWith(".gz")) {
val zcat = new Zcat(this)
@@ -159,14 +159,13 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val regex = """.*\/(.*)_vep_(\d*)_(.*)\.tar\.gz""".r
vepCacheUri.toString match {
- case regex(species, version, assembly) if (version.forall(_.isDigit)) => {
+ case regex(species, version, assembly) if version.forall(_.isDigit) =>
outputConfig ++= Map("varianteffectpredictor" -> Map(
"species" -> species,
"assembly" -> assembly,
"cache_version" -> version.toInt,
"cache" -> vepDir,
"fasta" -> createLinks(vepDir)))
- }
case _ => throw new IllegalArgumentException("Cache found but no version was found")
}
}
--
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