com.fulcrumgenomics.umi.CopyUmiFromReadName.scala Maven / Gradle / Ivy

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/*
 * The MIT License
 *
 * Copyright (c) 2022 Fulcrum Genomics
 *
 * 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.umi

import com.fulcrumgenomics.FgBioDef.{PathToBam, SafelyClosable}
import com.fulcrumgenomics.bam.api.{SamSource, SamWriter}
import com.fulcrumgenomics.cmdline.{ClpGroups, FgBioTool}
import com.fulcrumgenomics.commons.util.LazyLogging
import com.fulcrumgenomics.sopt.{arg, clp}
import com.fulcrumgenomics.util.{Io, ProgressLogger}

@clp(group=ClpGroups.Umi, description=
  """
    |Copies the UMI at the end of the BAM's read name to the RX tag.
    |
    |The read name is split on `:` characters with the last field assumed to be the UMI sequence.  The UMI
    |will be copied to the `RX` tag as per the SAM specification.  If any read does not have a UMI composed of
    |valid bases (ACGTN), the program will report the error and fail.
    |
    |If a read name contains multiple UMIs they may be delimited (typically by a hyphen (`-`) or plus (`+`)).
    |The `--umi-delimiter` option specifies the delimiter on which to split.  The resulting UMI in the `RX` tag
    |will always be hyphen delimited.
    |
    |Some tools (e.g. BCL Convert) may reverse-complement UMIs on R2 and add an 'r' prefix to indicate that the sequence
    |has been reverse-complemented.  By default, the 'r' prefix is removed and the sequence is reverse-complemented
    |back to the forward orientation.   The `--override-reverse-complement-umis` disables the latter behavior, such that
    |the 'r' prefix is removed but the UMI sequence is left as reverse-complemented.
  """)
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="Delimiter between the read name and UMI.") fieldDelimiter: Char = ':',
  @arg(doc="Delimiter between UMI sequences.") umiDelimiter: Char = '+',
  @arg(doc="Do not reverse-complement UMIs prefixed with 'r'.") overrideReverseComplementUmis: Boolean = false,
) extends FgBioTool with LazyLogging {

  Io.assertReadable(input)
  Io.assertCanWriteFile(output)

  override def execute(): Unit = {
    val source   = SamSource(input)
    val writer   = SamWriter(output, source.header)
    val progress = new ProgressLogger(logger)
    source.foreach { rec =>
      progress.record(rec)

      writer += Umis.copyUmiFromReadName(
        rec                           = rec, 
        removeUmi                     = removeUmi,
        fieldDelimiter                = fieldDelimiter,
        umiDelimiter                  = umiDelimiter,
        reverseComplementPrefixedUmis = !overrideReverseComplementUmis,
      )
    }
    progress.logLast()
    source.safelyClose()
    writer.close()
  }
}