chore: increase test coverage further

clintval · Jul 28, 2024 · 667578f · 667578f
1 parent 7b3ccbe
commit 667578f
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Showing 3 changed files with 4 additions and 1 deletion.
diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala
@@ -168,10 +168,12 @@ object Disambiguate {
     IOUtil.setCompressionLevel(conf.compression())
     Io.compressionLevel = conf.compression()
 
+    // $COVERAGE-OFF$
     if (IntelCompressionLibrarySupported) {
       BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory)
       BlockGunzipper.setDefaultInflaterFactory(new IntelInflaterFactory)
     }
+    // $COVERAGE-ON$
 
     Io.tmpDir = conf.tmpDir()
     System.setProperty("java.io.tmpdir", conf.tmpDir().toAbsolutePath.toString)

diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/TemplateOrdering.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/TemplateOrdering.scala
@@ -27,10 +27,12 @@ object TemplateOrdering extends FgBioEnum[TemplateOrdering] {
     * If neither template is clearly better, then the templates are equivalent.
     */
   case object ClassicOrdering extends TemplateOrdering {
+    // $COVERAGE-OFF$
     private def bestAlignmentScore(template: Template): MetricPair[Int]  = MetricPair[Int](template, AS)(_ max _)
     private def worstAlignmentScore(template: Template): MetricPair[Int] = MetricPair[Int](template, AS)(_ min _)
     private def bestNumMismatches(template: Template): MetricPair[Int]   = MetricPair[Int](template, NM)(_ min _)
     private def worstNumMismatches(template: Template): MetricPair[Int]  = MetricPair[Int](template, NM)(_ max _)
+    // $COVERAGE-ON$
 
     /** Compare two templates using the original published algorithm. */
     override def compare(x: Template, y: Template): Int = {

diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/bam/Bams.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/bam/Bams.scala
@@ -64,7 +64,6 @@ object Bams {
 
       /** Advance to the next sequence of templates. */
       override def next(): Seq[Template] = {
-        require(hasNext, "next() called on empty iterator")
         val templates = iterators.map(_.next())
         require(
           templates.map(_.name).distinct.length <= 1,