From 25aaee6ed731600a867677a7993d6f09902df116 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 8 Apr 2015 15:10:29 +0200
Subject: [PATCH] Try to convert numeric values appropriately in Picard metrics
parsing
---
.../picard/CollectAlignmentSummaryMetrics.scala | 2 +-
.../sasc/biopet/extensions/picard/MarkDuplicates.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/picard/Picard.scala | 8 +++++---
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 10cae9a65..541ee75b8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -70,7 +70,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
case None => Map()
case Some((header, content)) =>
(for (category <- 0 until content.size) yield {
- content(category)(0) -> (
+ content(category)(0).toString -> (
for (
i <- 1 until header.size if i < content(category).size
) yield {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 5a3121221..52777a467 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -103,7 +103,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
case None => Map()
case Some((header, content)) =>
(for (category <- 0 until content.size) yield {
- content(category)(0) -> (
+ content(category)(0).toString -> (
for (
i <- 1 until header.size if i < content(category).size
) yield {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index 064a182e3..03f7ba975 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -21,6 +21,7 @@ import scala.io.Source
import org.broadinstitute.gatk.utils.commandline.Argument
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.tryToParseNumber
/**
* General picard extension
@@ -80,7 +81,7 @@ object Picard {
* @param file input metrics file
* @return (header, content)
*/
- def getMetrics(file: File): Option[(Array[String], List[Array[String]])] =
+ def getMetrics(file: File): Option[(Array[String], List[Array[Any]])] =
if (file.exists) {
val lines = Source.fromFile(file).getLines().toArray
@@ -88,9 +89,10 @@ object Picard {
val end = lines.indexOf("", start)
val header = lines(start).split("\t")
- val content = (for (i <- (start + 1) until end) yield lines(i).split("\t")).toList
+ val content = (for (i <- (start + 1) until end) yield lines(i).split("\t"))
+ .map(row => row.map(col => tryToParseNumber(col).getOrElse(col)))
- Option((header, content))
+ Option((header, content.toList))
} else {
None
}
--
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