Commit 19323af6 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-259' into 'develop'

Fixed error message in bamutils

Fixes #259 

See merge request !311
parents ac55539b a13b0d1d
...@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan { ...@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
var vcfSampleList: Option[File] = config("vcf_sample_list") var vcfSampleList: Option[File] = config("vcf_sample_list")
var variants: Option[Int] = config("variants") var variants: Option[Int] = config("variants")
override def defaultCoreMemory = 6.0
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
val validValues: Set[Int] = Set(0, 1) val validValues: Set[Int] = Set(0, 1)
// check for boolean vars that are passed as ints // check for boolean vars that are passed as ints
......
...@@ -15,20 +15,15 @@ ...@@ -15,20 +15,15 @@
*/ */
package nl.lumc.sasc.biopet.extensions.varscan package nl.lumc.sasc.biopet.extensions.varscan
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.{ Version, BiopetJavaCommandLineFunction }
abstract class Varscan extends BiopetJavaCommandLineFunction { abstract class Varscan extends BiopetJavaCommandLineFunction with Version {
override def subPath = "varscan" :: super.subPath override def subPath = "varscan" :: super.subPath
jarFile = config("varscan_jar") jarFile = config("varscan_jar")
/** def versionCommand = super.commandLine
* TODO: test version def versionRegex = """VarScan v(.*)""".r
* override def versionCommand = super.commandLine
* override val versionRegex = """VarScan v(.*)""".r
*/
override def defaultCoreMemory = 5.0
} }
...@@ -25,7 +25,8 @@ object BamUtils { ...@@ -25,7 +25,8 @@ object BamUtils {
val inputSam = SamReaderFactory.makeDefault.open(file) val inputSam = SamReaderFactory.makeDefault.open(file)
val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
if (samples.size == 1) samples.head -> file if (samples.size == 1) samples.head -> file
else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file) else if (samples.size > 1) throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
else throw new IllegalArgumentException("Bam does not contain sample ID or have no readgroups defined: " + file)
} }
if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice") if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
temp.toMap temp.toMap
......
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