From 848279f41f5bb54b0dc141f6ab22cde21d176a32 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 23:02:46 +0100
Subject: [PATCH] Formatting updates
---
.../scala/nl/lumc/sasc/biopet/extensions/Sickle.scala | 8 ++++----
.../extensions/picard/CollectRnaSeqMetrics.scala | 2 +-
.../lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 11 ++++++-----
3 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index b030d3960..3d9fba0cc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -96,8 +96,8 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
line match {
// single run
- case sKept(num) => stats += ("num_reads_kept" -> num.toInt)
- case sDiscarded(num) => stats += ("num_reads_discarded_total" -> num.toInt)
+ case sKept(num) => stats += ("num_reads_kept" -> num.toInt)
+ case sDiscarded(num) => stats += ("num_reads_discarded_total" -> num.toInt)
// paired run
case pPairKept(reads, pairs) => stats += ("num_reads_kept" -> reads.toInt)
case pSingleKept(total, r1, r2) => {
@@ -116,8 +116,8 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
if (stats.contains("num_reads_discarded_both")) {
stats += ("num_reads_discarded_total" -> {
stats.getOrElse("num_reads_discarded_R1", 0) + stats.getOrElse("num_reads_discarded_R2", 0) +
- stats.getOrElse("num_reads_discarded_both", 0)
- })
+ stats.getOrElse("num_reads_discarded_both", 0)
+ })
}
stats.toMap
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 663525efd..baa4debcd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -79,7 +79,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
case None => Map()
case Some((header, content)) =>
(for (i <- 0 to header.size if i < content.head.size)
- yield header(i).toLowerCase -> content.head(i)).toMap
+ yield header(i).toLowerCase -> content.head(i)).toMap
}
override def commandLine = super.commandLine +
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 56e61a164..ecf4cb15f 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -90,7 +90,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
"format" -> "sam"
),
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
- "picard" -> Map (
+ "picard" -> Map(
"programrecordid" -> "null"
)
), super.defaults)
@@ -709,16 +709,17 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
add(sampleAlnJob)
// general RNA-seq metrics, if there are > 1 library
collectRnaSeqMetricsJob match {
- case Some(j) => add(j); addSummarizable(j, "rna_metrics")
- case None => ;
+ case Some(j) =>
+ add(j); addSummarizable(j, "rna_metrics")
+ case None => ;
}
bamMetricsModule match {
- case Some(m) =>
+ case Some(m) =>
m.init()
m.biopetScript()
addAll(m.functions)
addSummaryQScript(m)
- case None => ;
+ case None => ;
}
// add strand-specific jobs if defined
alnPlusStrandJobs.foreach(_.addAllJobs())
--
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