From 0499783ff1a964d9604b140124f316df197481df Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 3 Sep 2015 15:50:31 +0200
Subject: [PATCH] VcfWithVCf refactor
---
.../lumc/sasc/biopet/tools/VcfWithVcf.scala | 127 +++++++++++++-----
1 file changed, 90 insertions(+), 37 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 ef67616f2..15c71efa6 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
@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
+import java.util
-import htsjdk.variant.variantcontext.VariantContextBuilder
+import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf._
import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
@@ -25,6 +26,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
+import scala.collection.JavaConverters._
/**
* Biopet extension for tool VcfWithVcf
@@ -140,44 +142,11 @@ object VcfWithVcf extends ToolCommand {
var counter = 0
for (record <- reader) {
- val secondaryRecords = if (commandArgs.matchAllele) {
- secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
- filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
- } else {
- secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
- }
+ val secondaryRecords = getSecondaryRecords(secondaryReader, record, commandArgs.matchAllele)
- val fieldMap = (for (
- f <- commandArgs.fields if secondaryRecords.exists(_.hasAttribute(f.inputField))
- ) yield {
- f.outputField -> (for (
- secondRecord <- secondaryRecords if secondRecord.hasAttribute(f.inputField)
- ) yield {
- secondRecord.getAttribute(f.inputField) match {
- case l: List[_] => l
- case x => List(x)
- }
- }).fold(Nil)(_ ::: _)
- }).toMap
+ val fieldMap = createFieldMap(commandArgs.fields, secondaryRecords)
- writer.add(fieldMap.foldLeft(new VariantContextBuilder(record))((builder, attribute) => {
- builder.attribute(attribute._1, commandArgs.fields.filter(_.outputField == attribute._1).head.fieldMethod match {
- case FieldMethod.max =>
- header.getInfoHeaderLine(attribute._1).getType match {
- case VCFHeaderLineType.Integer => Array(attribute._2.map(_.toString.toInt).max)
- case VCFHeaderLineType.Float => Array(attribute._2.map(_.toString.toFloat).max)
- case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
- }
- case FieldMethod.min =>
- header.getInfoHeaderLine(attribute._1).getType match {
- case VCFHeaderLineType.Integer => Array(attribute._2.map(_.toString.toInt).min)
- case VCFHeaderLineType.Float => Array(attribute._2.map(_.toString.toFloat).min)
- case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
- }
- case FieldMethod.unique => attribute._2.distinct.toArray
- case _ => attribute._2.toArray
- })
- }).make())
+ writer.add(createRecord(fieldMap, record, commandArgs.fields, header))
counter += 1
if (counter % 100000 == 0) {
@@ -192,4 +161,88 @@ object VcfWithVcf extends ToolCommand {
secondaryReader.close()
logger.info("Done")
}
+
+
+ /**
+ * Create Map of field -> List of attributes in secondary records
+ * @param fields List of Field
+ * @param secondaryRecords List of VariantContext with secondary records
+ * @return Map of fields and their values in secondary records
+ */
+ def createFieldMap(fields: List[Fields], secondaryRecords: List[VariantContext]) : Map[String, List[Any]] = {
+ val fieldMap = (for (
+ f <- fields if secondaryRecords.exists(_.hasAttribute(f.inputField))
+ ) yield {
+ f.outputField -> (for (
+ secondRecord <- secondaryRecords if secondRecord.hasAttribute(f.inputField)
+ ) yield {
+ secondRecord.getAttribute(f.inputField) match {
+ case l: List[_] => l
+ case x => List(x)
+ }
+ }).fold(Nil)(_ ::: _)
+ }).toMap
+ fieldMap
+ }
+
+ /**
+ * Get secondary records matching the query record
+ * @param secondaryReader reader for secondary records
+ * @param record query record
+ * @param matchAllele allele has to match query allele?
+ * @return List of VariantContext
+ */
+ def getSecondaryRecords(secondaryReader: VCFFileReader,
+ record: VariantContext, matchAllele: Boolean) : List[VariantContext] = {
+ if (matchAllele) {
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
+ filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
+ } else {
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
+ }
+ }
+
+ def createRecord(fieldMap: Map[String, List[Any]], record: VariantContext,
+ fields: List[Fields], header: VCFHeader): VariantContext = {
+ fieldMap.foldLeft(new VariantContextBuilder(record))((builder, attribute) => {
+ builder.attribute(attribute._1, fields.filter(_.outputField == attribute._1).head.fieldMethod match {
+ case FieldMethod.max =>
+ header.getInfoHeaderLine(attribute._1).getType match {
+ case VCFHeaderLineType.Integer => sL2JOAL(List(attribute._2.map(_.toString.toInt).max))
+ case VCFHeaderLineType.Float => sL2JOAL(List(attribute._2.map(_.toString.toFloat).max))
+ case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
+ }
+ case FieldMethod.min =>
+ header.getInfoHeaderLine(attribute._1).getType match {
+ case VCFHeaderLineType.Integer => sL2JOAL(List(attribute._2.map(_.toString.toInt).min))
+ case VCFHeaderLineType.Float => sL2JOAL(List(attribute._2.map(_.toString.toFloat).min))
+ case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
+ }
+ case FieldMethod.unique => sL2JOAL(attribute._2.distinct)
+ case _ => sL2JOAL(attribute._2)
+ })
+ }).make()
+ }
+
+
+ /**
+ * HACK!!
+ * Stands for scalaListToJavaObjectArrayList
+ * Convert a scala List[Any] to a java ArrayList[Object]. This is necessary for BCF conversions
+ * As scala ints and floats cannot be directly cast to java objects (they aren't objects),
+ * we need to box them.
+ * For items not int and float, we assume them to be strings (TODO: sane assumption?)
+ * @param array scala List[Any]
+ * @return converted java ArrayList[Object]
+ */
+ private def sL2JOAL(array: List[Any]): util.ArrayList[Object] = {
+ val out = new util.ArrayList[Object]()
+
+ array.foreach {
+ case x: Int => out.add(Int.box(x))
+ case x: Float => out.add(Float.box(x))
+ case x => out.add(x.toString)
+ }
+ out
+ }
}
--
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