feat: add --umi-prefix to CopyUmiFromReadName

src/main/scala/com/fulcrumgenomics/umi/CopyUmiFromReadName.scala

@@ -42,11 +42,16 @@ import com.fulcrumgenomics.util.{Io, ProgressLogger}
     |
     |If a read name contains multiple UMIs they may be delimited by either hyphens (`-`) or pluses (`+`). The
     |resulting UMI in the `RX` tag will always be hyphen delimited.
+    |
+    |To obtain behavior similar to `umi_tools`' `--umi-separator=":r"`, specify the delimiter and
+    |prefix separately, i.e. `--umi-delimiter=":"` and `--umi-prefix="r"`.
   """)
 class CopyUmiFromReadName
 ( @arg(flag='i', doc="The input BAM file") input: PathToBam,
   @arg(flag='o', doc="The output BAM file") output: PathToBam,
-  @arg(doc="Remove the UMI from the read name") removeUmi: Boolean = false
+  @arg(doc="Remove the UMI from the read name") removeUmi: Boolean = false,
+  @arg(doc="Delimiter between the read name and UMI.") umiDelimiter: Char = ':',
+  @arg(doc="Any characters preceding the UMI sequence in the read name.") umiPrefix: Option[String] = None,
 ) extends FgBioTool with LazyLogging {
 
   Io.assertReadable(input)
@@ -58,7 +63,7 @@ class CopyUmiFromReadName
     val progress = new ProgressLogger(logger)
     source.foreach { rec =>
       progress.record(rec)
-      writer += Umis.copyUmiFromReadName(rec=rec, removeUmi=removeUmi)
+      writer += Umis.copyUmiFromReadName(rec=rec, removeUmi=removeUmi, delimiter=umiDelimiter, prefix=umiPrefix)
     }
     progress.logLast()
     source.safelyClose()

src/main/scala/com/fulcrumgenomics/umi/Umis.scala

@@ -41,9 +41,9 @@ object Umis {
     * @param delimiter the delimiter of fields within the read name
     * @return the modified record
     */
-  def copyUmiFromReadName(rec: SamRecord, removeUmi: Boolean = false, delimiter: Char = ':'): SamRecord = {
+  def copyUmiFromReadName(rec: SamRecord, removeUmi: Boolean = false, delimiter: Char = ':', prefix: Option[String] = None): SamRecord = {
     // Extract and set the UMI
-    val umi = extractUmisFromReadName(rec.name, delimiter, strict=false)
+    val umi = extractUmisFromReadName(rec.name, delimiter, strict=false, prefix=prefix)
     require(umi.nonEmpty, f"No valid UMI found in: ${rec.name}")
     umi.foreach(u => rec(ConsensusTags.UmiBases) = u)
 
@@ -67,7 +67,7 @@ object Umis {
     * 
     * If `strict` is false the last segment is returned so long as it appears to be a valid UMI.
     */
-  def extractUmisFromReadName(name: String, delimiter: Char = ':', strict: Boolean): Option[String] = {
+  def extractUmisFromReadName(name: String, delimiter: Char = ':', strict: Boolean, prefix: Option[String] = None): Option[String] = {
     // If strict, check that the read name actually has eight parts, which is expected
     val rawUmi = if (strict) {
       val colons = name.count(_ == delimiter)
@@ -80,8 +80,9 @@ object Umis {
       Some(name.substring(idx + 1, name.length))
     }
 
-    val umi   = rawUmi.map(raw => (if (raw.indexOf('+') > 0) raw.replace('+', '-') else raw).toUpperCase)
-    val valid = umi.forall(u => u.forall(isValidUmiCharacter))
+    val umiSeq = rawUmi.map(seq => (if (prefix.isEmpty) seq else seq.stripPrefix(prefix.get)))
+    val umi = umiSeq.map(raw => (if (raw.indexOf('+') > 0) raw.replace('+', '-') else raw).toUpperCase)
+    val valid  = umi.forall(u => u.forall(isValidUmiCharacter))
 
     if (strict && !valid) throw new IllegalArgumentException(s"Invalid UMI '${umi.get}' extracted from name '${name}")
     else if (!valid) None

src/test/scala/com/fulcrumgenomics/umi/CopyUmiFromReadNameTest.scala

@@ -33,14 +33,14 @@ class CopyUmiFromReadNameTest extends UnitSpec with OptionValues {
   private case class Result(name: String, umi: String)
 
   /** Runs CopyUmiFromReadName using the given read names returning the output read names and UMIs. */
-  private def run(names: Iterable[String], removeUmi: Boolean): IndexedSeq[Result] = {
+  private def run(names: Iterable[String], removeUmi: Boolean, umiPrefix: Option[String] = None): IndexedSeq[Result] = {
     // build the reads
     val builder = new SamBuilder()
     names.foreach { name => builder.addFrag(name=name, unmapped=true) }
 
     // run the tool
     val out  = makeTempFile("test.", ".bam")
-    val tool = new CopyUmiFromReadName(input=builder.toTempFile(), output=out, removeUmi=removeUmi)
+    val tool = new CopyUmiFromReadName(input=builder.toTempFile(), output=out, removeUmi=removeUmi, umiPrefix=umiPrefix)
     executeFgbioTool(tool)
 
     // slurp the results
@@ -69,4 +69,11 @@ class CopyUmiFromReadNameTest extends UnitSpec with OptionValues {
     results.map(_.name) should contain theSameElementsInOrderAs Seq("1", "1:2", "1:2:3", "blah")
     results.map(_.umi) should contain theSameElementsInOrderAs Seq("AAAA", "CCCC", "GGGG", "AAAA-CCCC")
   }
+
+  it should "remove any additional separator characters preceding the UMI" in {
+    val names   = Seq("1:rAAAA", "1:2:rCCCC", "1:2:3:rGGGG", "blah:rAAAA-CCCC")
+    val results = run(names=names, removeUmi=true, umiPrefix=Some("r"))
+    results.map(_.name) should contain theSameElementsInOrderAs Seq("1", "1:2", "1:2:3", "blah")
+    results.map(_.umi) should contain theSameElementsInOrderAs Seq("AAAA", "CCCC", "GGGG", "AAAA-CCCC")
+  }
 }