From 9123df3211fb13ef1d5966c10a5d8ea83a42fede Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 13 Feb 2015 17:28:03 +0100
Subject: [PATCH] Make better use of the File object, let the file object
concat the paths for me
---
.../biopet/pipelines/kopisu/ConiferPipeline.scala | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
index 54926853c..5e9355172 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
@@ -80,7 +80,7 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
val coniferRPKM = new ConiferRPKM(this)
coniferRPKM.bamFile = this.inputBam.getAbsoluteFile
coniferRPKM.probes = this.probeFile
- coniferRPKM.output = new File(RPKMdir + File.separator + input2RPKM(inputBam))
+ coniferRPKM.output = new File(RPKMdir, input2RPKM(inputBam))
add(coniferRPKM)
if (!RPKMonly) {
@@ -88,9 +88,10 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
var refRPKMlist: List[File] = Nil
// Sync the .txt only, these files contain the RPKM Values
for (controlRPKMfile <- controlsDir.list.filter(_.toLowerCase.endsWith(".txt"))) {
- val target = new File(RPKMdir + File.separator + controlRPKMfile.getName)
- val source = new File(controlsDir + File.separator + controlRPKMfile)
- if (!target.exists()) {
+ val target = new File(RPKMdir, controlRPKMfile)
+ val source = new File(controlsDir, controlRPKMfile)
+
+ if (!target.exists) {
add(Ln(this, source, target, false))
refRPKMlist :+= target
} else if (!target.equals(source)) {
@@ -104,18 +105,18 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
coniferAnalyze.deps = List(coniferRPKM.output) ++ refRPKMlist
coniferAnalyze.probes = this.probeFile
coniferAnalyze.rpkmDir = RPKMdir
- coniferAnalyze.output = new File(sampleDir + File.separator + input2HDF5(inputBam))
+ coniferAnalyze.output = new File(sampleDir, input2HDF5(inputBam))
add(coniferAnalyze)
val coniferCall = new ConiferCall(this)
coniferCall.input = coniferAnalyze.output
- coniferCall.output = new File(sampleDir + File.separator + "calls.txt")
+ coniferCall.output = new File(sampleDir, "calls.txt")
add(coniferCall)
summary.deps = List(coniferCall.output)
summary.label = sampleLabel
summary.calls = coniferCall.output
- summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
+ summary.out = new File(sampleDir, input2Calls(inputBam))
add(summary)
}
--
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