diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
similarity index 97%
rename from public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
rename to public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index eceb5b60ff0b6d33d2102a11334cc3b646d1d61b..f3bbea7c7c21d73744c7d2adf94f9876527427b3 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* Based on version 0.2.5b8
*/
-class Pindel(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
executable = config("exe", default = "pindel", freeVar = false)
override def defaultCoreMemory = 3.0
@@ -169,9 +169,9 @@ class Pindel(val root: Configurable) extends BiopetCommandLineFunction with Refe
optional("--DD_REPORT_DUPLICATION_READS", DD_REPORT_DUPLICATION_READS) +
}
-object Pindel {
- def apply(root: Configurable, configFile: File, outputDir: File): Pindel = {
- val caller = new Pindel(root)
+object PindelCaller {
+ def apply(root: Configurable, configFile: File, outputDir: File): PindelCaller = {
+ val caller = new PindelCaller(root)
caller.config_file = Some(configFile)
caller.output_prefix = outputDir
caller
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
index 77ab79f1e513f087d967d72ce757f8a0d1b95853..cef1c6ea23c25aec10a74d5a2311d86c48baf8ff 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
@@ -15,8 +15,9 @@
*/
package nl.lumc.sasc.biopet.extensions.pindel
-import java.io.File
+import java.io.{PrintWriter, File}
+import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -31,35 +32,20 @@ class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction
var output: File = _
@Argument(doc = "Insertsize")
- var insertsize: Option[Int] = _
+ var insertsize: Int = _
+
+ var sampleName: String = _
override def cmdLine = super.cmdLine +
"-i" + required(input) +
+ "-l" + required(sampleName) +
"-s" + required(insertsize) +
"-o" + required(output)
}
object PindelConfig extends ToolCommand {
- def apply(root: Configurable, input: File, output: File): PindelConfig = {
- val conf = new PindelConfig(root)
- conf.input = input
- conf.output = output
- conf
- }
-
- def apply(root: Configurable, input: File, outputDir: String): PindelConfig = {
- val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
- val outputFile = new File(dir + swapExtension(input.getName))
- apply(root, input, outputFile)
- }
-
- def apply(root: Configurable, input: File): PindelConfig = {
- apply(root, input, new File(swapExtension(input.getAbsolutePath)))
- }
-
- private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.cfg"
-
- case class Args(inputbam: File = null, samplelabel: Option[String] = None, insertsize: Option[Int] = None) extends AbstractArgs
+ case class Args(inputbam: File = null, samplelabel: Option[String] = None,
+ insertsize: Option[Int] = None, output: Option[File] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('i', "inputbam") required () valueName "<bamfile/path>" action { (x, c) =>
@@ -71,6 +57,9 @@ object PindelConfig extends ToolCommand {
opt[Int]('s', "insertsize") valueName "<insertsize>" action { (x, c) =>
c.copy(insertsize = Some(x))
} text "Insertsize is missing"
+ opt[Int]('o', "output") valueName "<output>" action { (x, c) =>
+ c.copy(insertsize = Some(x))
+ } text "Output path is missing"
}
/**
@@ -81,10 +70,26 @@ object PindelConfig extends ToolCommand {
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val input: File = commandArgs.inputbam
+ val output: File = commandArgs.output.getOrElse( new File(input.getAbsoluteFile + ".pindel.cfg") )
+ val insertsize: Int = commandArgs.insertsize.getOrElse(0)
+
+
+ val bamReader = SamReaderFactory.makeDefault().open(input)
+ val writer = new PrintWriter(output)
+ var sampleName: String = ""
+ for( readgroup <- bamReader.getFileHeader.getReadGroups() ) {
+ val rg = bamReader.getFileHeader.getReadGroup( readgroup )
+ writer.write( s"${input.getAbsoluteFile}\t${insertsize}\t${rg.getSample}")
+ }
+ bamReader.close()
+ writer.close()
// the logic here is to pull the libraries stored in the bam file and output this to a pindel config file.
// see: http://gmt.genome.wustl.edu/packages/pindel/quick-start.html
// this is called bam-configuration file
+
+ // sampleLabel can be given from the commandline or read from the bam header
+
/**
* filename<tab>avg insert size<tab>sample_label or name for reporting
* tumor_sample_1222.bam<tab>250<tab>TUMOR_1222
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelPipeline.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelPipeline.scala
deleted file mode 100644
index e5d276727eda9104fefebddc303747200415c354..0000000000000000000000000000000000000000
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelPipeline.scala
+++ /dev/null
@@ -1,86 +0,0 @@
-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.extensions.pindel
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-/// Pindel is actually a mini pipeline executing binaries from the pindel package
-class PindelPipeline(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
-
- @Input(doc = "Input file (bam)")
- var input: File = _
-
- @Input(doc = "Reference Fasta file")
- var reference: File = _
-
- @Argument(doc = "Work directory")
- var workdir: String = _
-
- // @Output(doc = "Pindel VCF output")
- // lazy val outputvcf: File = {
- // new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
- // }
-
- @Output(doc = "Pindel config")
- lazy val configfile: File = {
- new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
- }
- @Output(doc = "Pindel raw output")
- lazy val outputvcf: File = {
- new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
- }
-
- override def init() {
- }
-
- def biopetScript() {
- // read config and set all parameters for the pipeline
- logger.info("Starting Pindel configuration")
-
- val cfg = PindelConfig(this, input, this.configfile)
- outputFiles += ("pindel_cfg" -> cfg.output)
- add(cfg)
-
- val output: File = this.outputvcf
- val pindel = Pindel(this, cfg.output, output)
- add(pindel)
- outputFiles += ("pindel_tsv" -> pindel.output)
-
- // val output_vcf: File = this.outputvcf
- // convert this tsv to vcf using the python script
-
- }
-
- // private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.tsv"
-}
-
-object PindelPipeline extends PipelineCommand {
- def apply(root: Configurable, input: File, reference: File, runDir: String): PindelPipeline = {
- val pindel = new PindelPipeline(root)
- pindel.input = input
- pindel.reference = reference
- pindel.workdir = runDir
- // run the following for activating the pipeline steps
- pindel.init()
- pindel.biopetScript()
- pindel
- }
-}
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
index a810b5257a94479e5e7125e6755722543457ec30..e97dfd5262ed2a12699f4e4fc900df4696e67aa9 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -43,7 +43,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
}
/** Variantcallers requested by the config */
- protected val configCallers: Set[String] = config("sv_callers", default = Set("breakdancer", "clever", "delly"))
+ protected val configCallers: Set[String] = config("sv_callers", default = Set("breakdancer", "clever", "delly", "pindel"))
/** This will add jobs for this pipeline */
def biopetScript(): Unit = {
@@ -66,7 +66,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
}
/** Will generate all available variantcallers */
- protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this))
+ protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this), new Pindel(this))
/** Location of summary file */
def summaryFile = new File(outputDir, "ShivaSvCalling.summary.json")
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
new file mode 100644
index 0000000000000000000000000000000000000000..17b669c089543b208e5bff7e06947b97b4d3b2e6
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -0,0 +1,83 @@
+/**
+ * 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.
+ */
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelCaller$, PindelConfig}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/// Pindel is actually a mini pipeline executing binaries from the pindel package
+class Pindel(val root: Configurable) extends SvCaller {
+ val name = "pindel"
+
+ def this() = this(null)
+//
+// @Input(doc = "Input file (bam)")
+// var input: File = _
+//
+// @Input(doc = "Reference Fasta file")
+// var reference: File = _
+//
+// @Argument(doc = "Work directory")
+// var workdir: String = _
+//
+// // @Output(doc = "Pindel VCF output")
+// // lazy val outputvcf: File = {
+// // new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
+// // }
+//
+// @Output(doc = "Pindel config")
+// def configfile: File = {
+// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
+// }
+// @Output(doc = "Pindel raw output")
+// def outputvcf: File = {
+// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
+// }
+
+ def biopetScript() {
+ for ((sample, bamFile) <- inputBams) {
+ val pindelDir = new File(outputDir, sample)
+
+ val config_file: File = new File( bamFile.getAbsolutePath + ".pindel.cfg" )
+ val cfg = new PindelConfig(this)
+ cfg.input = bamFile
+
+ // FIXME: get the real insert size of the bam (from bammetrics?)
+ cfg.insertsize = 500
+ cfg.sampleName = sample
+ cfg.output = config_file
+ add(cfg)
+
+ val pindel = PindelCaller(this, cfg.output, pindelDir)
+ add(pindel)
+ }
+
+ }
+}
+
+object Pindel extends PipelineCommand {
+ def apply(root: Configurable, input: File, reference: File, runDir: String): Pindel = {
+ val pindel = new Pindel(root)
+ // run the following for activating the pipeline steps
+ pindel.init()
+ pindel.biopetScript()
+ pindel
+ }
+}
\ No newline at end of file