From a1605bf28997aeaea178ef51042cd157b03b4bd5 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 26 Aug 2015 17:40:28 +0200
Subject: [PATCH] BiopetFlagStat testing
---
.../test/resources/flagstat_crossreport.txt | 15 +++++
.../src/test/resources/flagstat_crosstrue.txt | 15 +++++
.../src/test/resources/flagstat_report.txt | 48 +++++++++++++++
.../src/test/resources/flagstat_summary.txt | 16 +++++
.../biopet/tools/BiopetFlagstatTest.scala | 60 +++++++++++++++++++
5 files changed, 154 insertions(+)
create mode 100644 public/biopet-framework/src/test/resources/flagstat_crossreport.txt
create mode 100644 public/biopet-framework/src/test/resources/flagstat_crosstrue.txt
create mode 100644 public/biopet-framework/src/test/resources/flagstat_report.txt
create mode 100644 public/biopet-framework/src/test/resources/flagstat_summary.txt
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
diff --git a/public/biopet-framework/src/test/resources/flagstat_crossreport.txt b/public/biopet-framework/src/test/resources/flagstat_crossreport.txt
new file mode 100644
index 000000000..74eabb412
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/flagstat_crossreport.txt
@@ -0,0 +1,15 @@
+ #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
diff --git a/public/biopet-framework/src/test/resources/flagstat_crosstrue.txt b/public/biopet-framework/src/test/resources/flagstat_crosstrue.txt
new file mode 100644
index 000000000..dd05aed41
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/flagstat_crosstrue.txt
@@ -0,0 +1,15 @@
+ #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%
diff --git a/public/biopet-framework/src/test/resources/flagstat_report.txt b/public/biopet-framework/src/test/resources/flagstat_report.txt
new file mode 100644
index 000000000..acbe332a8
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/flagstat_report.txt
@@ -0,0 +1,48 @@
+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%
+
diff --git a/public/biopet-framework/src/test/resources/flagstat_summary.txt b/public/biopet-framework/src/test/resources/flagstat_summary.txt
new file mode 100644
index 000000000..e7984915c
--- /dev/null
+++ b/public/biopet-framework/src/test/resources/flagstat_summary.txt
@@ -0,0 +1,16 @@
+{
+ "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
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
new file mode 100644
index 000000000..9eeb9fa3c
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
@@ -0,0 +1,60 @@
+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))
+ }
+
+}
--
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