Command line tool to produce and print pairwise alignments.

src/main/scala/com/fulcrumgenomics/alignment/Alignment.scala

@@ -25,6 +25,7 @@
 package com.fulcrumgenomics.alignment
 
 import com.fulcrumgenomics.FgBioDef._
+import com.fulcrumgenomics.util.Sequences
 import htsjdk.samtools.{CigarElement, CigarOperator, SAMRecord, Cigar => HtsJdkCigar}
 
 import scala.collection.mutable.ArrayBuffer
@@ -484,4 +485,18 @@ case class Alignment(query: Array[Byte],
 
     copy(queryStart=qStart, targetStart=tStart, cigar=Cigar(elems.result()), score=0)
   }
+
+  /** Returns a version of the alignment where both sequences have been reverse complemented
+    * and the alignment has been reversed to match.
+    */
+  def revcomped: Alignment = {
+    val query = this.query.clone()
+    val target = this.target.clone()
+    Sequences.revcomp(query)
+    Sequences.revcomp(target)
+    val cigar = this.cigar.reverse
+    val qs = query.length  - (this.queryStart + this.cigar.lengthOnQuery - 1) + 1
+    val ts = target.length - (this.targetStart + this.cigar.lengthOnTarget - 1) + 1
+    Alignment(query, target, qs, ts, cigar, this.score)
+  }
 }

src/main/scala/com/fulcrumgenomics/personal/tfenne/PairwiseAlign.scala

@@ -0,0 +1,57 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2021 Fulcrum Genomics LLC
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package com.fulcrumgenomics.personal.tfenne
+
+import com.fulcrumgenomics.FgBioDef._
+import com.fulcrumgenomics.alignment.{Aligner, Mode}
+import com.fulcrumgenomics.cmdline.{ClpGroups, FgBioTool}
+import com.fulcrumgenomics.fastq.{FastqSource, FastqWriter}
+import com.fulcrumgenomics.sopt.{arg, clp}
+import com.fulcrumgenomics.util.{Io, Sequences}
+
+@clp(group=ClpGroups.Personal, description=
+  """
+    |Align one query sequence to one target sequence.
+  """)
+class PairwiseAlign
+( @arg(flag='q', doc="Query sequence.")  val query: String,
+  @arg(flag='t', doc="Target sequence.") val target: String,
+  @arg(flag='m', doc="Alignment mode.") val mode: Mode = Mode.Global,
+) extends FgBioTool {
+
+  override def execute(): Unit = {
+    val aligner = Aligner(1, -4, -6, -1, mode)
+
+    val left  = aligner.align(query, target)
+    val right = aligner.align(Sequences.revcomp(query), Sequences.revcomp(target)).revcomped
+
+    println("Left Aligned:")
+    left.paddedString().foreach(println)
+
+    println()
+    println("Right Aligned:")
+    right.paddedString().foreach(println)
+  }
+}

src/test/scala/com/fulcrumgenomics/alignment/AlignmentTest.scala

@@ -280,6 +280,28 @@ class AlignmentTest extends UnitSpec {
     alignment.subByTarget(6, 10).cigar.toString() shouldBe "5D"
     alignment.subByTarget(6, 11).cigar.toString() shouldBe "5D1="
   }
+
+  "Alignment.revcomped" should "reverse complement a simple alignment" in {
+    val in = Alignment("TTTTT", "TTTTT", 1, 1, Cigar("5M"), 5)
+    val rc = in.revcomped
+    rc.query.map(_.toChar).mkString shouldBe "AAAAA"
+    rc.target.map(_.toChar).mkString shouldBe "AAAAA"
+    rc.queryStart shouldBe 1
+    rc.targetStart shouldBe 1
+    rc.cigar.toString shouldBe "5M"
+    rc.score shouldBe 5
+  }
+
+  it should "correctly reverse a non-global alignment" in {
+    val in = Alignment("..GTAACCGGTT".filter(_ != '.'), "ACGTAA.CGGTTCCCCC".filter(_ != '.'), 1, 3, Cigar("5M1I4M"), 10)
+    val rc = in.revcomped
+    rc.query.map(_.toChar).mkString shouldBe "AACCGGTTAC"
+    rc.target.map(_.toChar).mkString shouldBe "GGGGGAACCGTTACGT"
+    rc.queryStart shouldBe 1
+    rc.targetStart shouldBe 6
+    rc.cigar.toString shouldBe "4M1I5M"
+    rc.score shouldBe 10
+  }
 }
 
 class CigarStatsTest extends UnitSpec {