test proportion argument

fulcrumgenomics · Apr 3, 2024 · f6052af · f6052af
1 parent 9ccb1e6
commit f6052af
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Showing 2 changed files with 44 additions and 31 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/vcf/DownsampleVcf.scala b/src/main/scala/com/fulcrumgenomics/vcf/DownsampleVcf.scala
@@ -194,7 +194,7 @@ class DownsampleVcf
   @arg(flag='p', doc="Proportion of bases to retain (for single-sample VCF).") val proportion: Option[Double] = None,
   @arg(flag='b', doc="Original number of bases (for single-sample VCF).") val originalBases: Option[Double] = None,
   @arg(flag='m', doc="Index file with bases per sample.") val metadata: Option[FilePath] = None,
-  @arg(flag='n', doc="Target number of bases to downsample to.") val downsampleToBases: Option[Double],
+  @arg(flag='n', doc="Target number of bases to downsample to.") val downsampleToBases: Option[Double] = None,
   @arg(flag='o', doc="Output file name.") val output: PathToVcf,
   @arg(flag='w', doc="Winnowing window size.") val windowSize: Int = 0,
   @arg(flag='e', doc="Sequencing Error rate for genotyping.") val epsilon: Double = 0.01,

diff --git a/src/test/scala/com/fulcrumgenomics/vcf/DownsampleVcfTest.scala b/src/test/scala/com/fulcrumgenomics/vcf/DownsampleVcfTest.scala
@@ -369,22 +369,28 @@ class DownsampleVcfTest extends UnitSpec {
   Metric.write(metadata, Seq(Sample(SAMPLE_NAME = sample, BASE_COUNT = 100)))
 
   "DownsampleVcf" should "write a new vcf with downsampled genotypes when provided a vcf" in {
-    List(true, false).foreach(
-      use_metdata => {
+    List("proportion", "number", "metadata").foreach(
+      kind => {
         // Construct the input VCF
         val outVcf = makeTempFile("out", ".vcf.gz")
-        if(use_metdata) {
-          new DownsampleVcf(input=inVcf,
-                            output=outVcf,
-                            metadata=Some(metadata),
-                            downsampleToBases=Some(1),
-                            windowSize=150).execute()
-        } else {
-          new DownsampleVcf(input=inVcf,
-                            output=outVcf,
-                            originalBases=Some(100),
-                            downsampleToBases=Some(1),
-                            windowSize=150).execute()
+        kind match {
+          case "proportion" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              proportion=Some(0.01),
+                              windowSize=150).execute()
+          case "number" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              originalBases=Some(100),
+                              downsampleToBases=Some(1),
+                              windowSize=150).execute()
+          case "metadata" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              metadata=Some(metadata),
+                              downsampleToBases=Some(1),
+                              windowSize=150).execute()
         }
 
         val vs = readVcfRecs(outVcf)
@@ -428,24 +434,31 @@ class DownsampleVcfTest extends UnitSpec {
 
   "DownsampleVcf" should "write a new vcf with downsampled genotypes when provided a vcf, keeping nocalls" in {
     // Construct the input VCF
-    List(true, false).foreach(
-      use_metdata => {
+    List("proportion", "number", "metadata").foreach(
+      kind => {
         // Construct the input VCF
         val outVcf = makeTempFile("out", ".vcf.gz")
-        if (use_metdata) {
-          new DownsampleVcf(input=inVcf, 
-                            output=outVcf,
-                            metadata=Some(metadata),
-                            downsampleToBases=Some(1),
-                            writeNoCall=true,
-                            windowSize=150).execute()
-        } else {
-          new DownsampleVcf(input=inVcf,
-                            output=outVcf,
-                            originalBases=Some(100),
-                            downsampleToBases=Some(1),
-                            writeNoCall=true,
-                            windowSize=150).execute()
+        kind match {
+          case "proportion" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              proportion=Some(0.01),
+                              writeNoCall=true,
+                              windowSize=150).execute()
+          case "number" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              originalBases=Some(100),
+                              downsampleToBases=Some(1),
+                              writeNoCall=true,
+                              windowSize=150).execute()
+          case "metadata" =>
+            new DownsampleVcf(input=inVcf,
+                              output=outVcf,
+                              metadata=Some(metadata),
+                              downsampleToBases=Some(1),
+                              writeNoCall=true,
+                              windowSize=150).execute()
         }
 
         val vs = readVcfRecs(outVcf)