Commit 7f03f1ef authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing null pointer

parent 78159ed9
......@@ -154,7 +154,6 @@ class BamMetrics(val parent: Configurable) extends QScript
val biStrict = BedtoolsIntersect(this, inputBam, intervals.bed,
output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
minOverlap = config("strict_intersect_overlap", default = 1.0))
biStrict.jobOutputFile = new File(targetDir, ".biStrict.Bedtools.out")
val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
addSummarizable(biopetFlagstatStrict, targetName + "_flagstats_strict")
add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
......@@ -162,7 +161,6 @@ class BamMetrics(val parent: Configurable) extends QScript
val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
minOverlap = config("loose_intersect_overlap", default = 0.01))
biLoose.jobOutputFile = new File(targetDir, ".biLoose.Bedtools.out")
val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
addSummarizable(biopetFlagstatLoose, targetName + "_flagstats_loose")
add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
......
......@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph()
internalBeforeGraph()
this.commandDirectory = this.jobOutputFile.getParentFile
if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
super.freezeFieldValues()
}
......
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