diff --git a/src/test/scala/com/fulcrumgenomics/umi/UmiConsensusCallerTest.scala b/src/test/scala/com/fulcrumgenomics/umi/UmiConsensusCallerTest.scala index 99c5073b4..6e51da734 100644 --- a/src/test/scala/com/fulcrumgenomics/umi/UmiConsensusCallerTest.scala +++ b/src/test/scala/com/fulcrumgenomics/umi/UmiConsensusCallerTest.scala @@ -79,4 +79,14 @@ class UmiConsensusCallerTest extends UnitSpec with OptionValues { rg.getLibrary shouldBe "L1,L2" rg.getPlatform shouldBe "ILLUMINA" } + + "UmiConsensusCaller.toSourceRead" should "trim back the alignment if it extends past the mate" in { + val builder = new SamBuilder(sort=Some(SamOrder.TemplateCoordinate)) + val Seq(r1, r2) = builder.addPair(start1=100, start2=100, cigar1="20S80M", cigar2="10S90M") + val caller = new VanillaUmiConsensusCaller(readNamePrefix = "prefix") + val s1 = caller.toSourceRead(r1, minBaseQuality=0, trim=false).value + val s2 = caller.toSourceRead(r2, minBaseQuality=0, trim=false).value + s1.cigar.toString shouldBe "20S80M" + s2.cigar.toString shouldBe "90M" + } }