BiopetFlagStat testing

public/biopet-framework/src/test/resources/flagstat_crossreport.txt

+	#1	#2	#3	#4	#5	#6	#7	#8	#9	#10	#11	#12	#13	#14
+#1	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#2	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#4	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#5	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#6	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#7	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#8	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#9	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#10	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#11	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#12	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#13	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#14	0	0	0	0	0	0	0	0	0	0	0	0	0	0

public/biopet-framework/src/test/resources/flagstat_crosstrue.txt

+	#1	#2	#3	#4	#5	#6	#7	#8	#9	#10	#11	#12	#13	#14
+#1	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#2	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#3	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#4	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#5	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#6	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#7	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#8	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#9	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#10	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#11	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#12	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#13	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#14	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%

public/biopet-framework/src/test/resources/flagstat_report.txt

+Number	Total Flags	Fraction	Name
+#1	1	100.0000%	All
+#2	1	100.0000%	Mapped
+#3	0	0.0000%	Duplicates
+#4	1	100.0000%	FirstOfPair
+#5	0	0.0000%	SecondOfPair
+#6	0	0.0000%	ReadNegativeStrand
+#7	0	0.0000%	NotPrimaryAlignment
+#8	1	100.0000%	ReadPaired
+#9	1	100.0000%	ProperPair
+#10	1	100.0000%	MateNegativeStrand
+#11	0	0.0000%	MateUnmapped
+#12	0	0.0000%	ReadFailsVendorQualityCheck
+#13	0	0.0000%	SupplementaryAlignment
+#14	0	0.0000%	SecondaryOrSupplementary
+
+	#1	#2	#3	#4	#5	#6	#7	#8	#9	#10	#11	#12	#13	#14
+#1	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#2	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#4	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#5	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#6	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#7	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#8	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#9	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#10	1	1	0	1	0	0	0	1	1	1	0	0	0	0
+#11	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#12	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#13	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+#14	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+
+	#1	#2	#3	#4	#5	#6	#7	#8	#9	#10	#11	#12	#13	#14
+#1	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#2	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#3	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#4	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#5	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#6	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#7	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#8	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#9	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#10	100.0000%	100.0000%	0.0000%	100.0000%	0.0000%	0.0000%	0.0000%	100.0000%	100.0000%	100.0000%	0.0000%	0.0000%	0.0000%	0.0000%
+#11	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#12	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#13	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+#14	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%	NaN%
+

public/biopet-framework/src/test/resources/flagstat_summary.txt

+{
+    "Duplicates" : 0,
+    "NotPrimaryAlignment" : 0,
+    "All" : 1,
+    "ReadNegativeStrand" : 0,
+    "ProperPair" : 1,
+    "MateUnmapped" : 0,
+    "ReadFailsVendorQualityCheck" : 0,
+    "Mapped" : 1,
+    "SupplementaryAlignment" : 0,
+    "MateNegativeStrand" : 1,
+    "FirstOfPair" : 1,
+    "ReadPaired" : 1,
+    "SecondaryOrSupplementary" : 0,
+    "SecondOfPair" : 0
+}
\ No newline at end of file

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.SamReaderFactory
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 26-8-15.
+ */
+class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  import BiopetFlagstat._
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val bam = new File(resourcePath("/paired01.bam"))
+  val report = new File(resourcePath("/flagstat_report.txt"))
+  val summary = new File(resourcePath("/flagstat_summary.txt"))
+  val crossReport = new File(resourcePath("/flagstat_crossreport.txt"))
+  val crossTrue = new File(resourcePath("/flagstat_crosstrue.txt"))
+
+  val record = SamReaderFactory.makeDefault().open(bam).iterator().next()
+  val processor = new FlagstatCollector
+  processor.loadDefaultFunctions()
+  processor.loadRecord(record)
+
+  @Test
+  def testReport()= {
+    processor.report shouldBe Source.fromFile(report).mkString
+  }
+
+  @Test
+  def testSummary() = {
+    processor.summary shouldBe Source.fromFile(summary).mkString
+  }
+
+  @Test
+  def testCrossReport() = {
+    processor.crossReport() shouldBe Source.fromFile(crossReport).mkString
+  }
+
+  @Test
+  def testCrossReportTrue() = {
+    processor.crossReport(true) shouldBe Source.fromFile(crossTrue).mkString
+  }
+
+  @Test
+  def testMain() = {
+    main(Array("-I", bam.getAbsolutePath))
+  }
+
+}