feat: SamSource.query should handle out of range queries

src/main/scala/com/fulcrumgenomics/bam/api/SamSource.scala

@@ -91,9 +91,16 @@ class SamSource private(private val reader: SamReader) extends View[SamRecord] w
   /** Returns an iterator over all the records in the source. */
   override def iterator: SamIterator = new SamIterator(reader.getFileHeader, reader.iterator())
 
+  private def newQueryInterval(region: Locatable): QueryInterval = {
+    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. */
   def query(regions: IterableOnce[Locatable], queryType: QueryType = QueryType.Overlapping): SamIterator = {
-    val queries = QueryInterval.optimizeIntervals(regions.iterator.map(l => new QueryInterval(dict(l.getContig).index, l.getStart, l.getEnd)).toArray)
+    val queries = QueryInterval.optimizeIntervals(regions.iterator.map(l => newQueryInterval(l)).toArray)
     val contained = queryType == QueryType.Contained
     new SamIterator(header, reader.query(queries, contained))
   }

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
@@ -164,4 +165,28 @@ class SamIoTest extends UnitSpec {
     filterCount shouldBe 10
     mapCount shouldBe 10
   }
+
+  "SamSource.query" should "" in {
+      val queryType = QueryType.Overlapping
+      val builder = new SamBuilder(readLength=10, baseQuality=20, sort=Some(SamOrder.Coordinate))
+      Range(0, 10).foreach { _ => builder.addFrag(start=100) }
+      val source = builder.toSource
+
+      // test a query before the contig start
+      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, 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, queryType).length shouldBe 10
+
+      // at the start and end     
+      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
+  }
 }