fixes

fulcrumgenomics · Feb 14, 2025 · a5037dc · a5037dc
1 parent 721d9a1
commit a5037dc
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Showing 2 changed files with 15 additions and 14 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/bam/api/SamSource.scala b/src/main/scala/com/fulcrumgenomics/bam/api/SamSource.scala
@@ -92,11 +92,10 @@ class SamSource private(private val reader: SamReader) extends View[SamRecord] w
   override def iterator: SamIterator = new SamIterator(reader.getFileHeader, reader.iterator())
 
   private def newQueryInterval(region: Locatable): QueryInterval = {
-    val contig      = dict(region.getContig)
-    val contigIndex = contig.index
-    val start       = Math.max(region.getStart, 1);
-    val end         = Math.min(region.getEnd, contig.length)
-    new QueryInterval(contigIndex, start, end)
+    val contig = dict(region.getContig)
+    val start  = Math.max(region.getStart, 1);
+    val end    = Math.min(region.getEnd, contig.length)
+    new QueryInterval(contig.index, start, end)
   }
 
   /** Returns an iterator over the records in the regions provided. */

diff --git a/src/test/scala/com/fulcrumgenomics/bam/api/SamIoTest.scala b/src/test/scala/com/fulcrumgenomics/bam/api/SamIoTest.scala
@@ -28,6 +28,7 @@ import java.nio.file.Files
 import java.util.concurrent.{Callable, Executors, TimeUnit}
 
 import com.fulcrumgenomics.FgBioDef._
+import com.fulcrumgenomics.bam.api.QueryType.QueryType
 import com.fulcrumgenomics.fasta.{SequenceDictionary, SequenceMetadata}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
 import com.fulcrumgenomics.util.Io
@@ -166,25 +167,26 @@ class SamIoTest extends UnitSpec {
   }
 
   "SamSource.query" should "" in {
+      val queryType = QueryType.Overlapping
       val builder = new SamBuilder(readLength=10, baseQuality=20)
       Range(0, 10).foreach { _ => builder.addFrag(start=100) }
       val source = builder.toSource
 
       // test a query before the contig start
-      source.query("chr1", 0, 1000).length shouldBe 10
-      source.query("chr1", -100, 1000).length shouldBe 10
+      source.query("chr1", 0, 1000, queryType).length shouldBe 10
+      source.query("chr1", -100, 1000, queryType).length shouldBe 10
 
       // test a query after the contig end
-      val contigEnd = builder.dict("chr1").length
-      source.query("chr1", 100, contigEnd+1).length shouldBe 10
-      source.query("chr1", 100, contigEnd+100).length shouldBe 10
+      val contigEnd = builder.dict("chr1", queryType).length
+      source.query("chr1", 100, contigEnd+1, queryType).length shouldBe 10
+      source.query("chr1", 100, contigEnd+100, queryType).length shouldBe 10
 
       // test a query both before and after the contig start and end respectively
-      source.query("chr1", -100, contigEnd+100).length shouldBe 10
+      source.query("chr1", -100, contigEnd+100, queryType).length shouldBe 10
 
       // at the start and end     
-      source.query("chr1", 1, 1000).length shouldBe 10 
-      source.query("chr1", 100, contigEnd).length shouldBe 10
-      source.query("chr1", 1, contigEnd).length shouldBe 10
+      source.query("chr1", 1, 1000, queryType).length shouldBe 10 
+      source.query("chr1", 100, contigEnd, queryType).length shouldBe 10
+      source.query("chr1", 1, contigEnd, queryType).length shouldBe 10
   }
 }