From 4faa97b25e4a0d7a8c426a9d7748f25574faef24 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 27 Aug 2015 15:43:04 +0200
Subject: [PATCH] FindRepeatsPacBioTest
---
.../biopet/tools/FindRepeatsPacBioTest.scala | 64 +++++++++++++++++++
1 file changed, 64 insertions(+)
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
new file mode 100644
index 000000000..af0243cda
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -0,0 +1,64 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.{SamReaderFactory, QueryInterval}
+import nl.lumc.sasc.biopet.tools.FastqSplitter._
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.immutable.Nil
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import FindRepeatsPacBio._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val bed = resourcePath("/rrna01.bed")
+ val bam = resourcePath("/paired01.bam")
+
+ @Test
+ def testMain() = {
+
+ val args = Array("-I", bam, "-b", bed)
+ main(args)
+ }
+
+ @Test
+ def testResult() = {
+ val samReader = SamReaderFactory.makeDefault().open(new File(bam))
+ val header = samReader.getFileHeader
+ val record = samReader.iterator().next()
+ val interval = new QueryInterval(header.getSequenceIndex("chrQ"), 50, 55)
+ val result = procesSamrecord(record, interval)
+
+ result.isEmpty shouldBe false
+
+ result.get.samRecord shouldEqual record
+ result.get.beginDel should be >= 0
+ result.get.endDel should be >= 0
+ }
+
+ @Test
+ def testResultObject = {
+ val record = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val result = new Result
+ result.samRecord = record
+
+ result.samRecord shouldEqual record
+ result.beginDel shouldBe 0
+ result.endDel shouldBe 0
+ result.dels shouldEqual Nil
+ result.ins shouldEqual Nil
+ }
+
+
+}
--
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