Commit 848279f4 authored by bow's avatar bow
Browse files

Formatting updates

parent 08018011
......@@ -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
......
......@@ -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 +
......
......@@ -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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