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Commit 628069f0 authored by Wai Yi Leung's avatar Wai Yi Leung
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Remove Yamsvp code and optimize BamUtils.

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protected/LICENSE deleted 120000 → 0
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biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt
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protected/LICENSE 0 → 100644
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Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
public/LICENSE deleted 120000 → 0
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biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt
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public/LICENSE 0 → 100644
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Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
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public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
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......@@ -76,7 +76,7 @@ object BamUtils {
val counts = baminsertsizes.flatMap(x => x)
if (counts.size != 0) {
counts.reduceLeft(_ + _) / counts.size
counts.sum / counts.size
} else {
0
}
......
public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala
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......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.utils
import java.io.File
import htsjdk.samtools._
import org.mockito.Mockito.{inOrder => inOrd}
import org.mockito.Mockito.{ inOrder => inOrd }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{BeforeClass, Test}
import org.testng.annotations.{ BeforeClass, Test }
/**
* Created by wyleung on 22-2-16.
......
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
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......@@ -25,8 +25,6 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
class Pindel(val root: Configurable) extends SvCaller {
val name = "pindel"
def this() = this(null)
/** Default pipeline config */
override def defaults = Map(
"pindelvcf" -> Map(
......
public/yamsvp/.gitignore deleted 100644 → 0
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/target/
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public/yamsvp/pom.xml deleted 100644 → 0
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<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<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>
<artifactId>Yamsvp</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>Yamsvp</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala deleted 100644 → 0
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/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
/*
* Structural variation calling
*/
package nl.lumc.sasc.biopet.pipelines.yamsvp
import java.io.File
import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import nl.lumc.sasc.biopet.extensions.sambamba.{SambambaMarkdup, SambambaMerge}
import nl.lumc.sasc.biopet.pipelines.shiva.Delly
import nl.lumc.sasc.biopet.utils.config.Configurable
//import nl.lumc.sasc.biopet.extensions.pindel.Pindel
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.engine.JobRunInfo
import org.broadinstitute.gatk.queue.function._
class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
def summaryFile = null
def summaryFiles = Map()
def summarySettings = Map()
var reference: File = config("reference")
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def summaryFiles = Map()
def summaryStats = Map()
val alignmentDir: String = sampleDir + "alignment/"
val svcallingDir: String = sampleDir + "svcalls/"
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
// val runDir: String = alignmentDir + "run_" + libraryId + "/"
def summaryFiles = Map()
def summaryStats = Map()
val mapping = new Mapping(qscript)
mapping.libId = Some(libraryId)
mapping.sampleId = Some(sampleId)
protected def addJobs(): Unit = {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
mapping.outputDir = libDir
mapping.init()
mapping.biopetScript()
qscript.addAll(mapping.functions)
}
}
protected def addJobs(): Unit = {
val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
val bamFile: File = if (libraryBamfiles.size == 1) {
val alignmentlink = Ln(qscript, libraryBamfiles.head,
alignmentDir + sampleId + ".merged.bam", relative = true)
alignmentlink.isIntermediate = true
add(alignmentlink)
alignmentlink.output
} else if (libraryBamfiles.size > 1) {
val mergeSamFiles = new SambambaMerge(qscript)
mergeSamFiles.input = libraryBamfiles
mergeSamFiles.output = sampleDir + sampleId + ".merged.bam"
mergeSamFiles.isIntermediate = true
add(mergeSamFiles)
mergeSamFiles.output
} else null
val bamMarkDup = SambambaMarkdup(qscript, bamFile)
add(bamMarkDup)
addAll(BamMetrics(qscript, bamMarkDup.output, alignmentDir + "metrics" + File.separator).functions)
// create an IGV TDF file
val tdfCount = IGVToolsCount(qscript, bamMarkDup.output, config("genome_name", default = "hg19"))
add(tdfCount)
/// bamfile will be used as input for the SV callers. First run Clever
// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
val cleverDir = svcallingDir + sampleId + ".clever/"
val clever = CleverCaller(qscript, bamMarkDup.output, qscript.reference, svcallingDir, cleverDir)
add(clever)
val clever_vcf = Ln(qscript, clever.outputvcf, svcallingDir + sampleId + ".clever.vcf", relative = true)
add(clever_vcf)
val breakdancerDir = svcallingDir + sampleId + ".breakdancer/"
val breakdancer = Breakdancer(qscript, bamMarkDup.output, qscript.reference, breakdancerDir)
addAll(breakdancer.functions)
val bd_vcf = Ln(qscript, breakdancer.outputvcf, svcallingDir + sampleId + ".breakdancer.vcf", relative = true)
add(bd_vcf)
val dellyDir = svcallingDir + sampleId + ".delly/"
val delly = Delly(qscript, bamMarkDup.output, dellyDir)
addAll(delly.functions)
val delly_vcf = Ln(qscript, delly.outputvcf, svcallingDir + sampleId + ".delly.vcf", relative = true)
add(delly_vcf)
// for pindel we should use per library config collected into one config file
// val pindelDir = svcallingDir + sampleID + ".pindel/"
// val pindel = Pindel(qscript, analysisBam, this.reference, pindelDir)
// sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
// addAll(pindel.functions)
//
// val pindel_vcf = Ln(qscript, pindel.outputvcf, svcallingDir + sampleID + ".pindel.vcf", relative = true)
// add(pindel_vcf)
//
}
}
def addMultiSampleJobs() = {}
def init() {
}
def biopetScript() {
logger.info("Starting YAM SV Pipeline")
addSamplesJobs()
}
override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
logger.info("YAM SV Pipeline has run .......................")
}
}
object Yamsvp extends PipelineCommand
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public/yamsvp/src_old/test/resources/log4j.properties deleted 100644 → 0
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#
# Biopet is built on top of GATK Queue for building bioinformatic
# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
# should also be able to execute Biopet tools and pipelines.
#
# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
#
# Contact us at: sasc@lumc.nl
#
# A dual licensing mode is applied. The source code within this project that are
# not part of GATK Queue is freely available for non-commercial use under an AGPL
# license; For commercial users or users who do not want to follow the AGPL
# license, please contact us to obtain a separate license.
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
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