Commit c1aee221 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fixing seqstat usage of outDir

parent 163386a3
......@@ -60,15 +60,14 @@ object Seqstat extends ToolCommand {
def apply(root: Configurable, input: File, output: File): Seqstat = {
val seqstat = new Seqstat(root)
seqstat.input = input
seqstat.output = output
seqstat.output = new File(output, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".seqstats.json")
seqstat
}
def apply(root: Configurable, fastqfile: File, outDir: String): Seqstat = {
val seqstat = new Seqstat(root)
val ext = fastqfile.getName.substring(fastqfile.getName.lastIndexOf("."))
seqstat.input = fastqfile
seqstat.output = new File(outDir + fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
seqstat.output = new File(outDir, fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
seqstat
}
......
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