Commit 93d87c58 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix small bug

parent bc9c1c28
......@@ -78,6 +78,8 @@ object ValidateFastq extends ToolCommand {
if (readFq2.map(_.hasNext) == Some(true))
throw new IllegalStateException("R2 has more reads then R1")
logger.info(s"Possible quality encodings found: ${getPossibleEncodings.mkString(", ")}")
logger.info(s"Done processing ${counter} fastq records, no errors found")
} catch {
case e: IllegalStateException =>
......@@ -85,8 +87,6 @@ object ValidateFastq extends ToolCommand {
logger.error(e.getMessage)
}
logger.info(s"Possible quality encodings found: ${getPossibleEncodings.mkString(", ")}")
//close both iterators
readFq1.close()
readFq2.foreach(_.close())
......@@ -127,7 +127,8 @@ object ValidateFastq extends ToolCommand {
if (min >= '@' && max <= 'h') buffer += "Illumina 1.3+"
if (min >= 'C' && max <= 'h') buffer += "Illumina 1.5+"
if (min >= '!' && max <= 'J') buffer += "Illumina 1.8+"
if (buffer.isEmpty) throw new IllegalStateException("No possible quality encoding found")
if (buffer.isEmpty)
throw new IllegalStateException(s"No possible quality encoding found. minQual: '$min', maxQual: '$max'")
case _ =>
}
buffer.toList
......
......@@ -69,8 +69,8 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
@Test def testMustHaveGenotypes() = {
/**
* This should simply not raise an exception
*/
* This should simply not raise an exception
*/
val tmp = File.createTempFile("VCfFilter", ".vcf.gz")
tmp.deleteOnExit()
val tmp_path = tmp.getAbsolutePath
......
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