From 1f5b341b8ddde154e201640ecfd61e7844f0b2c6 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 29 Oct 2014 08:33:06 +0100
Subject: [PATCH] More main test
---
.../tools/ExtractAlignedFastqUnitTest.scala | 22 +++++++++++++++++++
1 file changed, 22 insertions(+)
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 67a2a1e5a..adf0b6451 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
+ }
}
--
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