diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala index 67a2a1e5a51f14fa2e3777d87846a7d07dc3af15..adf0b6451530d6ad2161accd07f18c80464b54e0 100644 --- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala +++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala @@ -251,4 +251,26 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat parsed.inputFastq1.getPath should ===(resourcePath("/single01.fq")) parsed.outputFastq1.getPath should ===("/tmp/tm1.fq") } + + @Test def testMainMaximum() = { + val args = Array( + "-I", resourcePath("/paired01.bam"), + "--interval", "chrQ:1-400", + "-i", resourcePath("/paired01a.fq"), + "-j", resourcePath("/paired01b.fq"), + "-o", "/tmp/tm1.fq", + "-p", "/tmp/tm2.fq", + "-s", "2", + "-Q", "30" + ) + val parsed = parseArgs(args) + parsed.inputBam.getPath should ===(resourcePath("/paired01.bam")) + parsed.intervals shouldBe List("chrQ:1-400") + parsed.inputFastq1.getPath should ===(resourcePath("/paired01a.fq")) + parsed.inputFastq2.get.getPath should ===(resourcePath("/paired01b.fq")) + parsed.outputFastq1.getPath should ===("/tmp/tm1.fq") + parsed.outputFastq2.get.getPath should ===("/tmp/tm2.fq") + parsed.commonSuffixLength shouldBe 2 + parsed.minMapQ shouldBe 30 + } }