Commit f74579d3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed compile issues

parent 63547f9b
...@@ -95,7 +95,7 @@ object SummaryToTsv extends ToolCommand { ...@@ -95,7 +95,7 @@ object SummaryToTsv extends ToolCommand {
def fetchValues(summary: Summary, def fetchValues(summary: Summary,
paths: Map[String, Array[String]], paths: Map[String, Array[String]],
sample: Boolean = false, sample: Boolean = false,
lib: Boolean = lib = false): Map[String, Map[String, Option[Any]]] = { lib: Boolean = false): Map[String, Map[String, Option[Any]]] = {
for ((name, path) <- paths) for ((name, path) <- paths)
yield yield
name -> { name -> {
......
...@@ -101,14 +101,14 @@ object VcfWithVcf extends ToolCommand { ...@@ -101,14 +101,14 @@ object VcfWithVcf extends ToolCommand {
val header = reader.getFileHeader val header = reader.getFileHeader
val vcfDict = header.getSequenceDictionary match { val vcfDict = header.getSequenceDictionary match {
case r if r != null => case r if r != null =>
r.assertSameDictionary(referenceDict, ignoreOrder = true) r.assertSameDictionary(referenceDict, true)
r r
case _ => referenceDict case _ => referenceDict
} }
val secondHeader = secondaryReader.getFileHeader val secondHeader = secondaryReader.getFileHeader
secondHeader.getSequenceDictionary match { secondHeader.getSequenceDictionary match {
case r if r != null => r.assertSameDictionary(referenceDict, ignoreOrder = true) case r if r != null => r.assertSameDictionary(referenceDict, true)
case _ => case _ =>
} }
......
...@@ -95,7 +95,7 @@ object BamStats extends ToolCommand { ...@@ -95,7 +95,7 @@ object BamStats extends ToolCommand {
referenceFasta referenceFasta
.map { f => .map { f =>
samHeader.getSequenceDictionary.assertSameDictionary(FastaUtils.getCachedDict(f), samHeader.getSequenceDictionary.assertSameDictionary(FastaUtils.getCachedDict(f),
ignoreOrder = false) false)
FastaUtils.getCachedDict(f) FastaUtils.getCachedDict(f)
} }
.getOrElse(samHeader.getSequenceDictionary) .getOrElse(samHeader.getSequenceDictionary)
......
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