DEV: Implement imputation for VCF features

* Update python wrapper to include imputation strategy parameter

* Update scala API to pass imputation strategy to VCFFeatureSource

* Create functions to handle mode and zero imputation strategies

* Added imputation strategy to test cases

* Added imputation strategy to FeatureSource cli

* Remove sparkPar from test cases due to changes in class signature

* Updated DefVariantToFeatureConverterTest to use zeros imputation

Author: NickEdwards7502

python/varspark/core.py

@@ -56,15 +56,26 @@ def __init__(self, ss, silent=False):
                 "                                      /_/                         \n"
             )
 
-    @params(self=object, vcf_file_path=str, min_partitions=int)
-    def import_vcf(self, vcf_file_path, min_partitions=0):
-        """Import features from a VCF file."""
+    @params(self=object, vcf_file_path=str, imputation_strategy=Nullable(str))
+    def import_vcf(self, vcf_file_path, imputation_strategy="none"):
+        """Import features from a VCF file.
+        
+        :param vcf_file_path String: The file path for the vcf file to import
+        :param imputation_strategy String:
+            The imputation strategy to use. Options for imputation include:
+
+            - none: No imputation will be performed. Missing values will be replaced with -1 (not recommended unless there are no missing values)
+            - mode: Missing values will be replaced with the most commonly occuring value among that feature. Recommended option
+            - zeros: Missing values will be replaced with zeros. Faster than mode imputation
+        """
+        if imputation_strategy == "none":
+            print("WARNING: Imputation strategy is set to none - please ensure that there are no missing values in the data.")
         return FeatureSource(
             self._jvm,
             self._vs_api,
             self._jsql,
             self.sql,
-            self._jvsc.importVCF(vcf_file_path, min_partitions),
+            self._jvsc.importVCF(vcf_file_path, imputation_strategy),
         )
 
     @params(
@@ -76,7 +87,7 @@ def import_vcf(self, vcf_file_path, min_partitions=0):
     def import_covariates(self, cov_file_path, cov_types=None, transposed=False):
         """Import covariates from a CSV file.
 
-        :param cov_file_path: The file path for covariate csv file
+        :param cov_file_path String: The file path for covariate csv file
         :param cov_types Dict[String]:
             A dictionary specifying types for each covariate, where the key is the variable name
             and the value is the type. The value can be one of the following:

src/main/scala/au/csiro/variantspark/api/VSContext.scala

@@ -38,11 +38,11 @@ class VSContext(val spark: SparkSession) extends SqlContextHolder {
     * @param inputFile path to file or directory with VCF files to load
     * @return FeatureSource loaded from the VCF file
     */
-  def importVCF(inputFile: String, sparkPar: Int = 0): FeatureSource = {
+  def importVCF(inputFile: String, imputationStrategy: String = "none"): FeatureSource = {
     val vcfSource =
       VCFSource(sc, inputFile)
     //  VCFSource(sc.textFile(inputFile, if (sparkPar > 0) sparkPar else sc.defaultParallelism))
-    VCFFeatureSource(vcfSource)
+    VCFFeatureSource(vcfSource, imputationStrategy)
   }
 
   /** Import features from a CSV file

src/main/scala/au/csiro/variantspark/cli/CochranArmanCmd.scala

@@ -89,7 +89,7 @@ class CochranArmanCmd extends ArgsApp with SparkApp with Echoable with Logging w
       VCFSource(sc.textFile(inputFile, if (sparkPar > 0) sparkPar else sc.defaultParallelism))
     verbose(s"VCF Version: ${vcfSource.version}")
     verbose(s"VCF Header: ${vcfSource.header}")
-    VCFFeatureSource(vcfSource)
+    VCFFeatureSource(vcfSource, imputationStrategy = "none")
   }
 
   def loadCSV(): CsvFeatureSource = {

src/main/scala/au/csiro/variantspark/cli/FilterCmd.scala

@@ -30,7 +30,7 @@ class FilterCmd extends ArgsApp with TestArgs with SparkApp {
     logDebug(s"Running with filesystem: ${fs}, home: ${fs.getHomeDirectory}")
 
     val vcfSource = VCFSource(sc.textFile(inputFile))
-    val source = VCFFeatureSource(vcfSource)
+    val source = VCFFeatureSource(vcfSource, imputationStrategy = "none")
     val features = source.features.zipWithIndex().cache()
     val featureCount = features.count()
     println(s"No features: ${featureCount}")

src/main/scala/au/csiro/variantspark/cli/VcfToLabels.scala

@@ -27,7 +27,7 @@ class VcfToLabels extends ArgsApp with SparkApp {
     val version = vcfSource.version
     println(header)
     println(version)
-    val source = VCFFeatureSource(vcfSource)
+    val source = VCFFeatureSource(vcfSource, imputationStrategy = "none")
     val columns = source.features.take(limit)
     CSVUtils.withFile(new File(outputFile)) { writer =>
       writer.writeRow("" :: columns.map(_.label).toList)

src/main/scala/au/csiro/variantspark/cli/args/FeatureSourceArgs.scala

@@ -26,8 +26,8 @@ object VCFFeatureSourceFactory {
   val DEF_SEPARATOR: String = "_"
 }
 
-case class VCFFeatureSourceFactory(inputFile: String, isBiallelic: Option[Boolean],
-    separator: Option[String])
+case class VCFFeatureSourceFactory(inputFile: String, imputationStrategy: Option[String],
+    isBiallelic: Option[Boolean], separator: Option[String])
     extends FeatureSourceFactory with Echoable {
   def createSource(sparkArgs: SparkArgs): FeatureSource = {
     echo(s"Loading header from VCF file: ${inputFile}")
@@ -36,8 +36,8 @@ case class VCFFeatureSourceFactory(inputFile: String, isBiallelic: Option[Boolea
     verbose(s"VCF Header: ${vcfSource.header}")
 
     import VCFFeatureSourceFactory._
-    VCFFeatureSource(vcfSource, isBiallelic.getOrElse(DEF_IS_BIALLELIC),
-      separator.getOrElse(DEF_SEPARATOR))
+    VCFFeatureSource(vcfSource, imputationStrategy.getOrElse("none"),
+      isBiallelic.getOrElse(DEF_IS_BIALLELIC), separator.getOrElse(DEF_SEPARATOR))
   }
 }
 

src/main/scala/au/csiro/variantspark/input/VCFFeatureSource.scala

@@ -10,6 +10,8 @@ import au.csiro.variantspark.data.StdFeature
 
 trait VariantToFeatureConverter {
   def convert(vc: VariantContext): Feature
+  def convertModeImputed(vc: VariantContext): Feature
+  def convertZeroImputed(vc: VariantContext): Feature
 }
 
 case class DefVariantToFeatureConverter(biallelic: Boolean = false, separator: String = "_")
@@ -20,6 +22,18 @@ case class DefVariantToFeatureConverter(biallelic: Boolean = false, separator: S
     StdFeature.from(convertLabel(vc), BoundedOrdinalVariable(3), gts)
   }
 
+  def convertModeImputed(vc: VariantContext): Feature = {
+    val gts = vc.getGenotypes.iterator().asScala.map(convertGenotype).toArray
+    val modeImputedGts = ModeImputationStrategy(noLevels = 3).impute(gts)
+    StdFeature.from(convertLabel(vc), BoundedOrdinalVariable(3), modeImputedGts)
+  }
+
+  def convertZeroImputed(vc: VariantContext): Feature = {
+    val gts = vc.getGenotypes.iterator().asScala.map(convertGenotype).toArray
+    val zeroImputedGts = ZeroImputationStrategy.impute(gts)
+    StdFeature.from(convertLabel(vc), BoundedOrdinalVariable(3), zeroImputedGts)
+  }
+
   def convertLabel(vc: VariantContext): String = {
 
     if (biallelic && !vc.isBiallelic) {
@@ -44,23 +58,34 @@ case class DefVariantToFeatureConverter(biallelic: Boolean = false, separator: S
   }
 
   def convertGenotype(gt: Genotype): Byte = {
-    if (!gt.isCalled || gt.isHomRef) 0 else if (gt.isHomVar || gt.isHetNonRef) 2 else 1
+    if (!gt.isCalled) Missing.BYTE_NA_VALUE
+    else if (gt.isHomRef) 0
+    else if (gt.isHomVar || gt.isHetNonRef) 2
+    else 1
   }
 }
 
-class VCFFeatureSource(vcfSource: VCFSource, converter: VariantToFeatureConverter)
+class VCFFeatureSource(vcfSource: VCFSource, converter: VariantToFeatureConverter,
+    imputationStrategy: String)
     extends FeatureSource {
   override lazy val sampleNames: List[String] =
     vcfSource.header.getGenotypeSamples.asScala.toList
   override def features: RDD[Feature] = {
     val converterRef = converter
-    vcfSource.genotypes().map(converterRef.convert)
+    imputationStrategy match {
+      case "none" => vcfSource.genotypes().map(converterRef.convert)
+      case "mode" => vcfSource.genotypes().map(converterRef.convertModeImputed)
+      case "zeros" => vcfSource.genotypes().map(converterRef.convertZeroImputed)
+      case _ =>
+        throw new IllegalArgumentException(s"Unknown imputation strategy: $imputationStrategy")
+    }
   }
 }
 
 object VCFFeatureSource {
-  def apply(vcfSource: VCFSource, biallelic: Boolean = false,
+  def apply(vcfSource: VCFSource, imputationStrategy: String, biallelic: Boolean = false,
       separator: String = "_"): VCFFeatureSource = {
-    new VCFFeatureSource(vcfSource, DefVariantToFeatureConverter(biallelic, separator))
+    new VCFFeatureSource(vcfSource, DefVariantToFeatureConverter(biallelic, separator),
+      imputationStrategy)
   }
 }

src/test/scala/au/csiro/variantspark/input/DefVariantToFeatureConverterTest.scala

@@ -37,15 +37,15 @@ class DefVariantToFeatureConverterTest {
   @Test
   def testConvertsBialleicVariantCorrctly() {
     val converter = DefVariantToFeatureConverter(true, ":")
-    val result = converter.convert(bialellicVC)
+    val result = converter.convertZeroImputed(bialellicVC)
     assertEquals("chr1:10:T:A", result.label)
     assertArrayEquals(expectedEncodedGenotype, result.valueAsByteArray)
   }
 
   @Test
   def testConvertsMultialleicVariantCorrctly() {
     val converter = DefVariantToFeatureConverter(false)
-    val result = converter.convert(multialleciVC)
+    val result = converter.convertZeroImputed(multialleciVC)
     assertEquals("chr1_10_T_A|G", result.label)
     assertArrayEquals(expectedEncodedGenotype, result.valueAsByteArray)
   }

src/test/scala/au/csiro/variantspark/misc/CovariateReproducibilityTest.scala

@@ -28,7 +28,7 @@ class CovariateReproducibilityTest extends SparkTest {
   def testCovariateReproducibleResults() {
     implicit val vsContext = VSContext(spark)
     implicit val sqlContext = spark.sqlContext
-    val genotypes = vsContext.importVCF("data/chr22_1000.vcf", 3)
+    val genotypes = vsContext.importVCF("data/chr22_1000.vcf")
     val optVariableTypes = new ArrayList[String](Arrays.asList("CONTINUOUS", "ORDINAL(2)",
         "CONTINUOUS", "CONTINUOUS", "CONTINUOUS", "CONTINUOUS"))
     val covariates =

src/test/scala/au/csiro/variantspark/misc/ReproducibilityTest.scala

@@ -25,7 +25,7 @@ class ReproducibilityTest extends SparkTest {
   def testReproducibleResults() {
     implicit val vsContext = VSContext(spark)
     implicit val sqlContext = spark.sqlContext
-    val features = vsContext.importVCF("data/chr22_1000.vcf", 3)
+    val features = vsContext.importVCF("data/chr22_1000.vcf")
     val label = vsContext.loadLabel("data/chr22-labels.csv", "22_16051249")
     val params = RandomForestParams(seed = 13L)
     val rfModel1 = RFModelTrainer.trainModel(features, label, params, 40, 20)