chore: cleaned up the PR after review

fulcrumgenomics · Mar 12, 2022 · e66f09e · e66f09e
1 parent 1762908
commit e66f09e
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Showing 2 changed files with 16 additions and 8 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/vcf/api/VcfWriter.scala b/src/main/scala/com/fulcrumgenomics/vcf/api/VcfWriter.scala
@@ -58,7 +58,7 @@ object VcfWriter {
     *
     * If the path is meant to point to a regular file, then indexing will occur automatically. However, if the path
     * already exists and the path is not a file or symbolic link, then this function will assume the path is a named
-    * pipe (such as `/dev/null`) and indexing will not occur.
+    * pipe or device (such as `/dev/null`) and indexing will not occur.
     *
     * @param path the path to write to
     * @param header the header of the VCF
@@ -67,7 +67,7 @@ object VcfWriter {
   def apply(path: PathToVcf, header: VcfHeader, async: Boolean = DefaultUseAsyncIo): VcfWriter = {
     import com.fulcrumgenomics.fasta.Converters.ToSAMSequenceDictionary
     val javaHeader = VcfConversions.toJavaHeader(header)
-    require(!Files.isDirectory(path), "Input path cannot be a directory!")
+    require(!Files.isDirectory(path), s"Path cannot be a directory! Found $path")
 
     val builder = new VariantContextWriterBuilder()
       .setOutputPath(path)

diff --git a/src/test/scala/com/fulcrumgenomics/vcf/api/VcfIoTest.scala b/src/test/scala/com/fulcrumgenomics/vcf/api/VcfIoTest.scala
@@ -24,11 +24,12 @@
 
 package com.fulcrumgenomics.vcf.api
 
+import com.fulcrumgenomics.commons.CommonsDef.SafelyClosable
 import com.fulcrumgenomics.commons.io.{Io, PathUtil}
 import com.fulcrumgenomics.testing.VcfBuilder.Gt
 import com.fulcrumgenomics.testing.{UnitSpec, VcfBuilder}
 import com.fulcrumgenomics.vcf.api.Allele.NoCallAllele
-import htsjdk.samtools.util.FileExtensions.{BCF => BcfExtension, COMPRESSED_VCF => VcfGzExtension, TABIX_INDEX => TbiExtension, TRIBBLE_INDEX => IdxExtension, VCF => VcfExtension}
+import htsjdk.samtools.util.FileExtensions.{BCF => BcfExtension, COMPRESSED_VCF => VcfGzExtension, CSI => CsiExtensions, TABIX_INDEX => TbiExtension, TRIBBLE_INDEX => IdxExtension, VCF => VcfExtension}
 import org.scalatest.OptionValues
 
 import java.nio.file.Files
@@ -244,7 +245,9 @@ class VcfIoTest extends UnitSpec with OptionValues {
     val writer  = VcfWriter(output, header = builder.header)
     builder.add(chrom = "chr1", pos = 100, alleles = Seq("A", "C"), gts = Seq(Gt(sample = "sample", gt = "0/1")))
     writer.close()
-    Files.exists(PathUtil.replaceExtension(output, VcfExtension + IdxExtension)) shouldBe true
+    val source = VcfSource(output)
+    source.isQueryable shouldBe true
+    source.safelyClose()
   }
 
   it should "write a sibling index when writing to a compressed VCF file" in {
@@ -254,7 +257,9 @@ class VcfIoTest extends UnitSpec with OptionValues {
     val writer  = VcfWriter(output, header = builder.header)
     builder.add(chrom = "chr1", pos = 100, alleles = Seq("A", "C"), gts = Seq(Gt(sample = "sample", gt = "0/1")))
     writer.close()
-    Files.exists(PathUtil.replaceExtension(PathUtil.removeExtension(output), VcfGzExtension + TbiExtension)) shouldBe true
+    val source = VcfSource(output)
+    source.isQueryable shouldBe true
+    source.safelyClose()
   }
 
   it should "write a sibling index when writing to a BCF file" in {
@@ -264,7 +269,9 @@ class VcfIoTest extends UnitSpec with OptionValues {
     val writer  = VcfWriter(output, header = builder.header)
     builder.add(chrom = "chr1", pos = 100, alleles = Seq("A", "C"), gts = Seq(Gt(sample = "sample", gt = "0/1")))
     writer.close()
-    Files.exists(PathUtil.replaceExtension(output, BcfExtension + IdxExtension)) shouldBe true
+    val source = VcfSource(output)
+    source.isQueryable shouldBe true
+    source.safelyClose()
   }
 
   it should "not attempt to write a sibling index when streaming to a named pipe like '/dev/null'" in {
@@ -273,7 +280,8 @@ class VcfIoTest extends UnitSpec with OptionValues {
     val writer  = VcfWriter(Io.DevNull, header = builder.header)
     builder.add(chrom = "chr1", pos = 100, alleles = Seq("A", "C"), gts = Seq(Gt(sample = "sample", gt = "0/1")))
     noException shouldBe thrownBy { writer.write(builder.toSeq); writer.close() }
-    Files.exists(PathUtil.pathTo(Io.DevNull.getFileName.toString + IdxExtension)) shouldBe false
-    Files.exists(PathUtil.pathTo(Io.DevNull.getFileName.toString + TbiExtension)) shouldBe false
+    Files.exists(PathUtil.pathTo(Io.DevNull.getFileName.toString + CsiExtensions)) shouldBe false
+    Files.exists(PathUtil.pathTo(Io.DevNull.getFileName.toString + IdxExtension))  shouldBe false
+    Files.exists(PathUtil.pathTo(Io.DevNull.getFileName.toString + TbiExtension))  shouldBe false
   }
 }