Commit a1d89efc authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Catch nullpointers

parent 869fb362
......@@ -26,8 +26,6 @@ import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFun
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.utils.commandline.Argument
import scala.collection.mutable.ListBuffer
/** Base for biopet pipeline */
trait BiopetQScript extends Configurable with GatkLogging {
......@@ -100,13 +98,15 @@ trait BiopetQScript extends Configurable with GatkLogging {
inputFiles.foreach { i =>
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
else if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
}
functions.filter(_.jobOutputFile == null).foreach(f => {
if (f.jobOutputFile == null && f.firstOutput != null)
try {
f.jobOutputFile = new File(f.firstOutput.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + configName + ".out")
else throw new IllegalStateException(s"Can't generate a jobOutputFile for $f")
} catch {
case e: NullPointerException => logger.warn(s"Can't generate a jobOutputFile for $f")
}
})
if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
......
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