From 53782d969324e359c58eafd5373bedd8b080dea3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 14:34:14 +0200
Subject: [PATCH] Adding biopet extension for VcfWithVcf tool
---
.../lumc/sasc/biopet/tools/VcfWithVcf.scala | 54 ++++++++++++++++---
1 file changed, 46 insertions(+), 8 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 9009d2918..07681a738 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -20,10 +20,48 @@ import java.io.File
import htsjdk.variant.variantcontext.VariantContextBuilder
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
+/**
+ * Biopet extension for tool VcfWithVcf
+ */
+class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
+ javaMainClass = getClass.getName
+
+ @Input(doc = "Input vcf file", shortName = "input", required = true)
+ var input: List[File] = Nil
+
+ @Input(doc = "Secondary vcf file", shortName = "secondary", required = true)
+ var secondaryVcf: List[File] = Nil
+
+ @Output(doc = "Output vcf file", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "Output vcf file index", shortName = "output", required = true)
+ private var outputIndex: File = _
+
+ var fields: List[(String, String, Option[String])] = List()
+
+ override def defaultCoreMemory = 2.0
+
+ override def beforeGraph() {
+ super.beforeGraph()
+ if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+ if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+ if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
+ }
+
+ override def commandLine = super.commandLine +
+ repeat("-I", input) +
+ required("-o", output) +
+ required("-s", secondaryVcf) +
+ repeat("-f", fields.map(x => x._1 + ":" + x._2 + ":" + x._3.getOrElse("none")))
+}
+
/**
* This is a tool to annotate a vcf file with info value from a other vcf file
*
@@ -46,10 +84,10 @@ object VcfWithVcf extends ToolCommand {
opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
}
- opt[File]('O', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ opt[File]('o', "outputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = x)
}
- opt[File]('S', "secondaryVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ opt[File]('s', "secondaryVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(secondaryVcf = x)
}
opt[String]('f', "field") unbounded () valueName "<field> or <input_field:output_field> or <input_field:output_field:method>" action { (x, c) =>
@@ -58,11 +96,11 @@ object VcfWithVcf extends ToolCommand {
else if (values.size > 1) c.copy(fields = Fields(values(0), values(1)) :: c.fields)
else c.copy(fields = Fields(x, x) :: c.fields)
} text """| If only <field> is given, the field's identifier in the output VCF will be identical to <field>.
- | By default we will return all values found for a given field.
- | With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
- | - max : takes maximum of found value, only works for numeric (integer/float) fields
- | - min : takes minemal of found value, only works for numeric (integer/float) fields
- | - unique: takes only unique values """.stripMargin
+ | By default we will return all values found for a given field.
+ | With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
+ | - max : takes maximum of found value, only works for numeric (integer/float) fields
+ | - min : takes minemal of found value, only works for numeric (integer/float) fields
+ | - unique: takes only unique values """.stripMargin
opt[Boolean]("match") valueName "<Boolean>" maxOccurs 1 action { (x, c) =>
c.copy(matchAllele = x)
} text "Match alternative alleles; default true"
--
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