Add a read group (and sample) per read in a SAM/BAM

add_rg_per_read.sc

import $ivy.`com.fulcrumgenomics::fgbio:1.1.0`
import com.fulcrumgenomics.FgBioDef._
import java.nio.file.{Path, Paths}
import com.fulcrumgenomics.commons.util.{LazyLogging, Logger}
import com.fulcrumgenomics.util.ProgressLogger
import com.fulcrumgenomics.bam.api._
import htsjdk.samtools.SAMReadGroupRecord


// So that a [[Path]] can be built from a [[String]] on the command line
implicit val pathRead: scopt.Read[Path] = scopt.Read.reads(path => Paths.get(path))

// So we can have a logger.
private object AddRgPerRead extends LazyLogging {
  def toLogger: Logger = this.logger
}

@doc("Tags each read with its own read group")
@main
def main(in: PathToBam @doc("The input SAM/BAM file."),
         out: PathToBam@doc("The output SAM/BAM file.")): Unit = {
  val logger   = AddRgPerRead.toLogger
  val progress = ProgressLogger(logger, verb="Read", unit=500000)
  val source   = SamSource(in)
  val header   = source.header.clone()
  val records  = source.toSeq  // NB: loads all the reads into memory!

  // update the header
  val readGroups = records.map { rec => 
    val readGroup = new SAMReadGroupRecord(rec.name)
    readGroup.setSample(rec.name)
    readGroup
  }
  header.setReadGroups(readGroups.iterator.toJavaList)

  // write the records
  val writer = SamWriter(out, header)
  records.foreach { rec =>
    progress.record(rec)
    rec("RG") = rec.name
    writer += rec
  }
  progress.logLast()

  // clean up
  writer.close()
  source.safelyClose()
}