feat: add a tool to do a simple local pairwise alignment

Author: clintval

src/test/scala/com/fulcrumgenomics/bam/pileup/PileupBuilderTest.scala

@@ -323,6 +323,23 @@ class PileupBuilderTest extends UnitSpec {
       piler.safelyClose()
     }
 
+    it should "exclude records that appear to be in an FR pair but are on different chromosomes" in {
+      val builder = new SamBuilder(readLength = ReadLength, sd = Some(TestSequenceDictionary), sort = Some(Coordinate))
+
+      builder.addPair(name = "q1", contig1 = Chr1, contig2 = Chr2, start1 = 101, start2 = 300)
+
+      val source = builder.toSource
+      val piler  = PileupBuilder(source, accessPattern = accessPattern)
+
+      piler.pileup(Chr1, 100).depth shouldBe 0
+      piler.pileup(Chr1, 101).depth shouldBe 0
+      piler.pileup(Chr1, 100 + ReadLength - 1).depth shouldBe 0
+      piler.pileup(Chr1, 101 + ReadLength - 1).depth shouldBe 0
+
+      source.safelyClose()
+      piler.safelyClose()
+    }
+
     it should "not filter out records where a position is outside what might look like an 'insert' for a non-FR pair" in {
       val builder = new SamBuilder(readLength = ReadLength, sd = Some(TestSequenceDictionary), sort = Some(Coordinate))