diff --git a/biopet-framework/pom.xml b/biopet-framework/pom.xml
index 69c3c3ff4f7ac147c87ade7ec0c9a0c790090a33..ac2879e75dea217e25cc42adf3e9b0aae80cd277 100644
--- a/biopet-framework/pom.xml
+++ b/biopet-framework/pom.xml
@@ -1,36 +1,35 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
- <version>0.2.0-DEV</version>
- <packaging>jar</packaging>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetFramework</artifactId>
+ <version>0.2.0-DEV</version>
+ <packaging>jar</packaging>
- <name>BiopetFramework</name>
- <url>http://maven.apache.org</url>
+ <name>BiopetFramework</name>
+ <url>http://maven.apache.org</url>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <sting.unpack.phase>prepare-package</sting.unpack.phase>
+ <sting.shade.phase>package</sting.shade.phase>
+ <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
+ </properties>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <sting.unpack.phase>prepare-package</sting.unpack.phase>
- <sting.shade.phase>package</sting.shade.phase>
- <sting.binary-dist.name>SASC-Pipelines</sting.binary-dist.name>
- <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
- </properties>
-
<repositories>
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
- <url>http://www.biojava.org/download/maven/</url>
+ <url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
<dependencies>
<dependency>
- <groupId>org.testng</groupId>
- <artifactId>testng</artifactId>
- <version>6.8</version>
- <scope>test</scope>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
@@ -68,9 +67,9 @@
<version>18.0</version>
</dependency>
<dependency>
- <groupId>com.github.scopt</groupId>
- <artifactId>scopt_2.10</artifactId>
- <version>3.2.0</version>
+ <groupId>com.github.scopt</groupId>
+ <artifactId>scopt_2.10</artifactId>
+ <version>3.2.0</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
@@ -81,16 +80,16 @@
<build>
<resources>
<resource>
- <directory>src/main/scripts</directory>
- <includes>
- <include>**/*</include>
- </includes>
+ <directory>src/main/scripts</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
</resource>
<resource>
- <directory>src/main/resources</directory>
- <includes>
- <include>**/*</include>
- </includes>
+ <directory>src/main/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
</resource>
</resources>
<plugins>
@@ -102,7 +101,7 @@
<execution>
<goals>
<goal>revision</goal>
- </goals>
+ </goals>
</execution>
</executions>
@@ -141,9 +140,10 @@
</goals>
<configuration>
<args>
-<!-- <arg>-make:transitive</arg>-->
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
+ <arg>-deprecation</arg>
+ <arg>-feature</arg>
</args>
</configuration>
</execution>
@@ -154,7 +154,7 @@
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
- <archive>
+ <archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
@@ -163,50 +163,50 @@
</configuration>
</plugin>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-shade-plugin</artifactId>
- <version>2.3</version>
- <configuration>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.3</version>
+ <configuration>
<finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
<transformers>
- <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
- <manifestEntries>
- <Main-Class>${app.main.class}</Main-Class>
- <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
- <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
- </manifestEntries>
- </transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <manifestEntries>
+ <Main-Class>${app.main.class}</Main-Class>
+ <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+ <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+ </manifestEntries>
+ </transformer>
</transformers>
<filters>
<filter>
- <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
- <includes>
- <include>*/**</include>
- <include>org/simpleframework/**</include>
- <include>org/jets3t/**</include>
- <include>com/sun/**</include>
- <include>org/ggf/**</include>
- <include>picard/**</include>
- <include>htsjdk/**</include>
- <include>javassist/**</include>
- <include>com/google/**</include>
- <include>org/reflections/</include>
- <include>org/jgrapht/**</include>
- <include>org/broadinstitute/**</include>
- <include>org/apache/**</include>
- <include>scala/tools/nsc/reporters/**</include>
- </includes>
+ <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
+ <includes>
+ <include>*/**</include>
+ <include>org/simpleframework/**</include>
+ <include>org/jets3t/**</include>
+ <include>com/sun/**</include>
+ <include>org/ggf/**</include>
+ <include>picard/**</include>
+ <include>htsjdk/**</include>
+ <include>javassist/**</include>
+ <include>com/google/**</include>
+ <include>org/reflections/</include>
+ <include>org/jgrapht/**</include>
+ <include>org/broadinstitute/**</include>
+ <include>org/apache/**</include>
+ <include>scala/tools/nsc/reporters/**</include>
+ </includes>
</filter>
</filters>
- </configuration>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>shade</goal>
- </goals>
- </execution>
- </executions>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -221,33 +221,35 @@
<artifactId>scalariform-maven-plugin</artifactId>
<version>0.1.4</version>
<executions>
- <execution>
- <phase>process-sources</phase>
- <goals>
- <goal>format</goal>
- </goals>
- <configuration>
- <rewriteArrowSymbols>false</rewriteArrowSymbols>
- <alignParameters>true</alignParameters>
- <alignSingleLineCaseStatements_maxArrowIndent>40</alignSingleLineCaseStatements_maxArrowIndent>
- <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
- <compactStringConcatenation>false</compactStringConcatenation>
- <compactControlReadability>false</compactControlReadability>
- <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
- <formatXml>true</formatXml>
- <indentLocalDefs>false</indentLocalDefs>
- <indentPackageBlocks>true</indentPackageBlocks>
- <indentSpaces>2</indentSpaces>
- <placeScaladocAsterisksBeneathSecondAsterisk>false</placeScaladocAsterisksBeneathSecondAsterisk>
- <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
- <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
- <rewriteArrowSymbols>false</rewriteArrowSymbols>
- <spaceBeforeColon>false</spaceBeforeColon>
- <spaceInsideBrackets>false</spaceInsideBrackets>
- <spaceInsideParentheses>false</spaceInsideParentheses>
- <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
- </configuration>
- </execution>
+ <execution>
+ <phase>process-sources</phase>
+ <goals>
+ <goal>format</goal>
+ </goals>
+ <configuration>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <alignParameters>true</alignParameters>
+ <alignSingleLineCaseStatements_maxArrowIndent>40
+ </alignSingleLineCaseStatements_maxArrowIndent>
+ <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
+ <compactStringConcatenation>false</compactStringConcatenation>
+ <compactControlReadability>false</compactControlReadability>
+ <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
+ <formatXml>true</formatXml>
+ <indentLocalDefs>false</indentLocalDefs>
+ <indentPackageBlocks>true</indentPackageBlocks>
+ <indentSpaces>2</indentSpaces>
+ <placeScaladocAsterisksBeneathSecondAsterisk>false
+ </placeScaladocAsterisksBeneathSecondAsterisk>
+ <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
+ <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <spaceBeforeColon>false</spaceBeforeColon>
+ <spaceInsideBrackets>false</spaceInsideBrackets>
+ <spaceInsideParentheses>false</spaceInsideParentheses>
+ <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
+ </configuration>
+ </execution>
</executions>
</plugin>
</plugins>
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
index 253cab16b78908eee3e236bc323e0ed437449690..cc8bf6afe2ea4f8f4fa4856ccf2047273ec4957a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
@@ -1,7 +1,7 @@
package nl.lumc.sasc.biopet.extensions
import java.io.File
-import scala.sys.process.Process
+import scala.sys.process.{ Process, ProcessLogger }
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.config.Configurable
@@ -71,15 +71,21 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
if (relative) {
// workaround until we have `ln` that works with relative path (i.e. `ln -r`)
- "ln -s '" + inRelative + "' '" + outCanonical + "'"
+ "ln -s " + inRelative + " " + outCanonical
} else {
- "ln -s '" + inCanonical + "' '" + outCanonical + "'"
+ "ln -s " + inCanonical + " " + outCanonical
}
}
override def run {
- val process = Process(cmd).run
- logger.info("cmd: '" + cmd + "', exitcode: " + process.exitValue)
+ val stdout = new StringBuffer()
+ val stderr = new StringBuffer()
+ val process = Process(cmd).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
+ val exitcode = process.exitValue
+ if (exitcode != 0) {
+ throw new Exception("Error creating symbolic link, this was the original message: \n" + stderr)
+ }
+ logger.info("cmd: '" + cmd + "', exitcode: " + exitcode)
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index d0f09baaa820b1a57ed181f66c25996faf9330a6..7f7fe2239ba176f7b1ed9104c5f9e7a507f44760 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.ToolCommand
object ExtractAlignedFastq extends ToolCommand {
- type FastqPair = (FastqRecord, FastqRecord)
+ type FastqInput = (FastqRecord, Option[FastqRecord])
/**
* Function to create iterator over Interval given input interval string
@@ -74,7 +74,7 @@ object ExtractAlignedFastq extends ToolCommand {
def makeMembershipFunction(iv: Iterator[Interval],
inAln: File,
minMapQ: Int = 0,
- commonSuffixLength: Int = 0): (FastqPair => Boolean) = {
+ commonSuffixLength: Int = 0): (FastqInput => Boolean) = {
val inAlnReader = SamReaderFactory
.make()
@@ -112,54 +112,39 @@ object ExtractAlignedFastq extends ToolCommand {
}
)
- (pair: FastqPair) => pair._2 match {
- case null => selected.contains(pair._1.getReadHeader)
- case otherwise =>
+ (pair: FastqInput) => pair._2 match {
+ case None => selected.contains(pair._1.getReadHeader)
+ case Some(x) =>
require(commonSuffixLength < pair._1.getReadHeader.length)
- require(commonSuffixLength < pair._2.getReadHeader.length)
+ require(commonSuffixLength < x.getReadHeader.length)
selected.contains(pair._1.getReadHeader.dropRight(commonSuffixLength))
}
}
- def selectFastqReads(memFunc: FastqPair => Boolean,
- inputFastq1: FastqReader,
- outputFastq1: BasicFastqWriter,
- inputFastq2: FastqReader = null,
- outputFastq2: BasicFastqWriter = null): Unit = {
-
- val i1 = inputFastq1.iterator.asScala
- val i2 = inputFastq2 match {
- case null => Iterator.continually(null)
- case otherwise => otherwise.iterator.asScala
- }
- val o1 = outputFastq1
- val o2 = (inputFastq2, outputFastq2) match {
- case (null, null) => null
- case (_, null) => throw new IllegalArgumentException("Missing output FASTQ 2")
- case (null, _) => throw new IllegalArgumentException("Output FASTQ 2 supplied but there is no input FASTQ 2")
- case (x, y) => outputFastq2
- }
-
- logger.info("Writing output file(s) ...")
- // zip, filter based on function, and write to output file(s)
- i1.zip(i2)
+ def extractReads(memFunc: FastqInput => Boolean,
+ inputFastq1: FastqReader, outputFastq1: BasicFastqWriter): Unit =
+ inputFastq1.iterator.asScala
+ .zip(Iterator.continually(None))
.filter(rec => memFunc(rec._1, rec._2))
- .foreach {
- case (rec1, null) =>
- o1.write(rec1)
- case (rec1, rec2) =>
- o1.write(rec1)
- o2.write(rec2)
- }
-
- }
-
- case class Args(inputBam: File = null,
+ .foreach(rec => outputFastq1.write(rec._1))
+
+ def extractReads(memFunc: FastqInput => Boolean,
+ inputFastq1: FastqReader, outputFastq1: BasicFastqWriter,
+ inputFastq2: FastqReader, outputFastq2: BasicFastqWriter): Unit =
+ inputFastq1.iterator.asScala
+ .zip(inputFastq2.iterator.asScala)
+ .filter(rec => memFunc(rec._1, Some(rec._2)))
+ .foreach(rec => {
+ outputFastq1.write(rec._1)
+ outputFastq2.write(rec._2)
+ })
+
+ case class Args(inputBam: File = new File(""),
intervals: List[String] = List.empty[String],
- inputFastq1: File = null,
- inputFastq2: File = null,
- outputFastq1: File = null,
- outputFastq2: File = null,
+ inputFastq1: File = new File(""),
+ inputFastq2: Option[File] = None,
+ outputFastq1: File = new File(""),
+ outputFastq2: Option[File] = None,
minMapQ: Int = 0,
commonSuffixLength: Int = 0) extends AbstractArgs
@@ -188,7 +173,7 @@ object ExtractAlignedFastq extends ToolCommand {
} text "Input FASTQ file 1"
opt[File]('j', "in2") optional () valueName "<fastq>" action { (x, c) =>
- c.copy(inputFastq1 = x)
+ c.copy(inputFastq2 = Option(x))
} validate {
x => if (x.exists) success else failure("Input FASTQ file 2 not found")
} text "Input FASTQ file 2 (default: none)"
@@ -198,7 +183,7 @@ object ExtractAlignedFastq extends ToolCommand {
} text "Output FASTQ file 1"
opt[File]('p', "out2") optional () valueName "<fastq>" action { (x, c) =>
- c.copy(outputFastq1 = x)
+ c.copy(outputFastq2 = Option(x))
} text "Output FASTQ file 2 (default: none)"
opt[Int]('Q', "min_mapq") optional () action { (x, c) =>
@@ -215,35 +200,43 @@ object ExtractAlignedFastq extends ToolCommand {
""".stripMargin)
checkConfig { c =>
- if (!c.inputBam.exists)
- failure("Input BAM file not found")
- else if (!c.inputFastq1.exists)
- failure("Input FASTQ file 1 not found")
- else if (c.inputFastq2 != null && c.outputFastq2 == null)
+ if (c.inputFastq2 != None && c.outputFastq2 == None)
failure("Missing output FASTQ file 2")
- else if (c.inputFastq2 == null && c.outputFastq2 != null)
+ else if (c.inputFastq2 == None && c.outputFastq2 != None)
failure("Missing input FASTQ file 2")
else
success
}
}
- def main(args: Array[String]): Unit = {
-
- val commandArgs: Args = new OptParser()
+ def parseArgs(args: Array[String]): Args =
+ new OptParser()
.parse(args, Args())
.getOrElse(sys.exit(1))
+ def main(args: Array[String]): Unit = {
+
+ val commandArgs: Args = parseArgs(args)
+
val memFunc = makeMembershipFunction(
iv = makeIntervalFromString(commandArgs.intervals),
inAln = commandArgs.inputBam,
minMapQ = commandArgs.minMapQ,
commonSuffixLength = commandArgs.commonSuffixLength)
- selectFastqReads(memFunc,
- inputFastq1 = new FastqReader(commandArgs.inputFastq1),
- inputFastq2 = new FastqReader(commandArgs.inputFastq2),
- outputFastq1 = new BasicFastqWriter(commandArgs.outputFastq1),
- outputFastq2 = new BasicFastqWriter(commandArgs.outputFastq2))
+ (commandArgs.inputFastq2, commandArgs.outputFastq2) match {
+
+ case (None, None) => extractReads(memFunc,
+ new FastqReader(commandArgs.inputFastq1),
+ new BasicFastqWriter(commandArgs.inputFastq1))
+
+ case (Some(i2), Some(o2)) => extractReads(memFunc,
+ new FastqReader(commandArgs.inputFastq1),
+ new BasicFastqWriter(commandArgs.outputFastq1),
+ new FastqReader(i2),
+ new BasicFastqWriter(o2))
+
+ case _ => // handled by the command line config check above
+ }
}
}
diff --git a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala
index 76c609094230185cead8dd01789b4604beb87342..04f6758ca3141c4c9910c10daeef2cadaaccc11b 100644
--- a/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala
+++ b/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala
@@ -19,7 +19,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/dir/nested/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s 'target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s target.txt /dir/nested/link.txt")
}
@Test(description = "Target is one level above link, relative set to true")
@@ -28,7 +28,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/dir/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s '../target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s ../target.txt /dir/nested/link.txt")
}
@Test(description = "Target is two levels above link, relative set to true")
@@ -37,7 +37,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s '../../target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s ../../target.txt /dir/nested/link.txt")
}
@Test(description = "Target is a child of a directory one level above link, relative set to true")
@@ -46,7 +46,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/dir/another_nested/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s '../another_nested/target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s ../another_nested/target.txt /dir/nested/link.txt")
}
@Test(description = "Target is one level below link, relative set to true")
@@ -55,7 +55,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/dir/nested/deeper/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s 'deeper/target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s deeper/target.txt /dir/nested/link.txt")
}
@Test(description = "Target is two levels below link, relative set to true")
@@ -64,7 +64,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = true
ln.in = new File("/dir/nested/even/deeper/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s 'even/deeper/target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s even/deeper/target.txt /dir/nested/link.txt")
}
@Test(description = "Relative set to false")
@@ -73,7 +73,7 @@ class LnUnitTest extends TestNGSuite with Matchers {
ln.relative = false
ln.in = new File("/dir/nested/target.txt")
ln.out = new File("/dir/nested/link.txt")
- ln.cmd should ===("ln -s '/dir/nested/target.txt' '/dir/nested/link.txt'")
+ ln.cmd should ===("ln -s /dir/nested/target.txt /dir/nested/link.txt")
}
// TODO: test for case where abosolute is true and input paths are relative?
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 19b05904b6135df1576d334668a4338494e6bd7f..4cd7205c0ac6e22c4f93c384600c9f570bc88c06 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
@@ -8,7 +8,7 @@ import java.io.File
import java.nio.file.Paths
import org.mockito.Matchers._
-import org.mockito.Mockito._
+import org.mockito.Mockito.{ inOrder => inOrd, times, verify }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
@@ -22,7 +22,10 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
import ExtractAlignedFastq._
private def resourceFile(p: String): File =
- new File(Paths.get(getClass.getResource(p).toURI).toString)
+ new File(resourcePath(p))
+
+ private def resourcePath(p: String): String =
+ Paths.get(getClass.getResource(p).toURI).toString
private def makeInterval(chr: String, start: Int, end: Int): Interval =
new Interval(chr, start, end)
@@ -30,11 +33,11 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
private def makeRecord(header: String): FastqRecord =
new FastqRecord(header, "ATGC", "", "HIHI")
- private def makeSingleRecords(headers: String*): Map[String, FastqPair] =
- headers.map(x => (x, (makeRecord(x), null))).toMap
+ private def makeSingleRecords(headers: String*): Map[String, FastqInput] =
+ headers.map(x => (x, (makeRecord(x), None))).toMap
- private def makePairRecords(headers: (String, (String, String))*): Map[String, FastqPair] =
- headers.map(x => (x._1, (makeRecord(x._2._1), makeRecord(x._2._2)))).toMap
+ private def makePairRecords(headers: (String, (String, String))*): Map[String, FastqInput] =
+ headers.map(x => (x._1, (makeRecord(x._2._1), Some(makeRecord(x._2._2))))).toMap
private def makeClue(tName: String, f: File, rName: String): String =
tName + " on " + f.getName + ", read " + rName + ": "
@@ -109,7 +112,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
@Test(dataProvider = "singleAlnProvider1")
def testSingleBamDefault(name: String, feat: Interval, inAln: File,
- fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+ fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
val memFunc = makeMembershipFunction(Iterator(feat), inAln)
for ((key, (rec1, rec2)) <- fastqMap) {
@@ -137,7 +140,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
@Test(dataProvider = "singleAlnProvider2")
def testSingleBamMinMapQ(name: String, feat: Interval, inAln: File, minMapQ: Int,
- fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+ fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
val memFunc = makeMembershipFunction(Iterator(feat), inAln, minMapQ)
for ((key, (rec1, rec2)) <- fastqMap) {
@@ -175,7 +178,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
@Test(dataProvider = "pairAlnProvider1")
def testPairBamDefault(name: String, feat: Interval, inAln: File,
- fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+ fastqMap: Map[String, FastqInput], resultMap: Map[String, Boolean]) = {
require(resultMap.keySet == fastqMap.keySet)
val memFunc = makeMembershipFunction(Iterator(feat), inAln, commonSuffixLength = 2)
for ((key, (rec1, rec2)) <- fastqMap) {
@@ -185,53 +188,68 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Mat
}
}
- @Test def testWriteSingleBamDefault() = {
- val memFunc = (recs: FastqPair) => Set("r01", "r03").contains(recs._1.getReadHeader)
+ @Test def testWriteSingleFastqDefault() = {
+ val memFunc = (recs: FastqInput) => Set("r01", "r03").contains(recs._1.getReadHeader)
val in1 = new FastqReader(resourceFile("/single01.fq"))
val mo1 = mock[BasicFastqWriter]
- selectFastqReads(memFunc, in1, mo1)
+ val obs = inOrd(mo1)
+ extractReads(memFunc, in1, mo1)
verify(mo1, times(2)).write(anyObject.asInstanceOf[FastqRecord])
- verify(mo1).write(new FastqRecord("r01", "A", "", "H"))
- verify(mo1).write(new FastqRecord("r03", "G", "", "H"))
+ obs.verify(mo1).write(new FastqRecord("r01", "A", "", "H"))
+ obs.verify(mo1).write(new FastqRecord("r03", "G", "", "H"))
}
- @Test def testWritePairBamDefault() = {
- val memFunc = (recs: FastqPair) => Set("r01/1", "r01/2", "r03/1", "r03/2").contains(recs._1.getReadHeader)
+ @Test def testWritePairFastqDefault() = {
+ val mockSet = Set("r01/1", "r01/2", "r03/1", "r03/2")
+ val memFunc = (recs: FastqInput) => mockSet.contains(recs._1.getReadHeader) || mockSet.contains(recs._2.get.getReadHeader)
val in1 = new FastqReader(resourceFile("/paired01a.fq"))
val in2 = new FastqReader(resourceFile("/paired01b.fq"))
val mo1 = mock[BasicFastqWriter]
val mo2 = mock[BasicFastqWriter]
- selectFastqReads(memFunc, in1, mo1, in2, mo2)
+ val obs = inOrd(mo1, mo2)
+ extractReads(memFunc, in1, mo1, in2, mo2)
+ obs.verify(mo1).write(new FastqRecord("r01/1", "A", "", "H"))
+ obs.verify(mo2).write(new FastqRecord("r01/2", "T", "", "I"))
+ obs.verify(mo1).write(new FastqRecord("r03/1", "G", "", "H"))
+ obs.verify(mo2).write(new FastqRecord("r03/2", "C", "", "I"))
verify(mo1, times(2)).write(anyObject.asInstanceOf[FastqRecord])
- verify(mo1).write(new FastqRecord("r01/1", "A", "", "H"))
- verify(mo1).write(new FastqRecord("r03/1", "G", "", "H"))
verify(mo2, times(2)).write(anyObject.asInstanceOf[FastqRecord])
- verify(mo2).write(new FastqRecord("r01/2", "T", "", "I"))
- verify(mo2).write(new FastqRecord("r03/2", "C", "", "I"))
- }
-
- @Test def testWriteNoOutputFastq2() = {
- val memFunc: (FastqPair => Boolean) = (recs) => true
- val in1 = mock[FastqReader]
- val in2 = mock[FastqReader]
- val out1 = mock[BasicFastqWriter]
- val thrown = intercept[IllegalArgumentException] {
- selectFastqReads(memFunc, in1, out1, in2)
- }
- thrown.getMessage should ===("Missing output FASTQ 2")
- verify(out1, never).write(anyObject.asInstanceOf[FastqRecord])
}
- @Test def testWriteNoInputFastq2() = {
- val memFunc: (FastqPair => Boolean) = (recs) => true
- val in1 = mock[FastqReader]
- val out1 = mock[BasicFastqWriter]
- val out2 = mock[BasicFastqWriter]
- val thrown = intercept[IllegalArgumentException] {
- selectFastqReads(memFunc, in1, out1, outputFastq2 = out2)
- }
- thrown.getMessage should ===("Output FASTQ 2 supplied but there is no input FASTQ 2")
- verify(out1, never).write(anyObject.asInstanceOf[FastqRecord])
- verify(out2, never).write(anyObject.asInstanceOf[FastqRecord])
+ @Test def testArgsMinimum() = {
+ val args = Array(
+ "-I", resourcePath("/single01.bam"),
+ "--interval", "chrQ:1-400",
+ "-i", resourcePath("/single01.fq"),
+ "-o", "/tmp/tm1.fq"
+ )
+ val parsed = parseArgs(args)
+ parsed.inputBam shouldBe resourceFile("/single01.bam")
+ parsed.intervals shouldBe List("chrQ:1-400")
+ parsed.inputFastq1 shouldBe resourceFile("/single01.fq")
+ parsed.outputFastq1 shouldBe new File("/tmp/tm1.fq")
+ }
+
+ @Test def testArgsMaximum() = {
+ val args = Array(
+ "-I", resourcePath("/paired01.bam"),
+ "--interval", "chrQ:1-400",
+ "--interval", "chrP:1000-4000",
+ "-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 shouldBe resourceFile("/paired01.bam")
+ parsed.intervals shouldBe List("chrQ:1-400", "chrP:1000-4000")
+ parsed.inputFastq1 shouldBe resourceFile("/paired01a.fq")
+ parsed.inputFastq2.get shouldBe resourceFile("/paired01b.fq")
+ parsed.outputFastq1 shouldBe new File("/tmp/tm1.fq")
+ parsed.outputFastq2.get shouldBe new File("/tmp/tm2.fq")
+ parsed.commonSuffixLength shouldBe 2
+ parsed.minMapQ shouldBe 30
}
}
diff --git a/pom.xml b/pom.xml
index 7e98eb6956a1390dff1a32cce1bf1ee28d581f46..732ff3d241c9af014fdd61b74aea83b3b091a430 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,12 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>Biopet</artifactId>
- <version>0.1.3</version>
- <packaging>pom</packaging>
- <name>Biopet</name>
- <modules>
- <module>biopet-framework</module>
- </modules>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Biopet</artifactId>
+ <version>0.2.0-DEV</version>
+ <packaging>pom</packaging>
+ <name>Biopet</name>
+ <modules>
+ <module>biopet-framework</module>
+ </modules>
</project>