packagenl.lumc.sasc.biopet.tools.bamstatsimportjava.io.Fileimportjava.nio.file.Pathsimportcom.google.common.io.Filesimportorg.scalatest.Matchersimportorg.scalatest.testng.TestNGSuiteimportorg.testng.annotations.Test/** * Created by pjvan_thof on 21-7-16. */classBamStatsTestextendsTestNGSuitewithMatchers{@TestdeftestMain:Unit={valoutputDir=Files.createTempDir()outputDir.deleteOnExit()BamStats.main(Array("-b",BamStatsTest.pairedBam01.getAbsolutePath,"-o",outputDir.getAbsolutePath))newFile(outputDir,"flagstats")shouldexistnewFile(outputDir,"flagstats.summary.json")shouldexistnewFile(outputDir,"mapping_quality.tsv")shouldexistnewFile(outputDir,"insert_size.tsv")shouldexistnewFile(outputDir,"clipping.tsv")shouldexistnewFile(outputDir,"left_clipping.tsv")shouldexistnewFile(outputDir,"right_clipping.tsv")shouldexistnewFile(outputDir,"5_prime_clipping.tsv")shouldexistnewFile(outputDir,"3_prime_clipping.tsv")shouldexist}}objectBamStatsTest{privatedefresourcePath(p:String):String={Paths.get(getClass.getResource(p).toURI).toString}valpairedBam01=newFile(resourcePath("/paired01.bam"))}