SamSourceUtil.scala

import com.fulcrumgenomics.bam.api.SamSource
import com.fulcrumgenomics.commons.CommonsDef._

/** Namespace for SAM/BAM source utilities. */
object SamSourceUtil {

  /** Return the only sample in this SAM/BAM source otherwise raise an exception. */
  def onlySample(source: SamSource): String = {
    validateHasSingleSample(source)
    source.header.getReadGroups.map(_.getSample).toSeq.head
  }

  /** Return the only sample in this SAM/BAM file otherwise raise an exception. */
  def onlySample(bam: PathToBam): String = {
    val source = SamSource(bam)
    yieldAndThen(onlySample(source))(source.safelyClose())
  }

  /** The sample names from the input SAM/BAM source. */
  def samples(source: SamSource): Seq[String] = {
    source.header.getReadGroups.map(_.getSample).distinct.toSeq
  }

  /** The sample names from the input SAM/BAM file. */
  def samples(sam: PathToBam): Seq[String] = {
    val source = SamSource(sam)
    yieldAndThen(samples(source))(source.safelyClose())
  }

  /** Validate that a SAM/BAM source has a single sample's reads.  */
  def validateHasSingleSample(source: SamSource): Unit = {
    val names = samples(source)
    val n     = names.length
    if (n != 1) {
      source.safelyClose()
      throw new IllegalArgumentException(s"SAM/BAM is not single-sample and has $n samples: ${names.mkString(", ")}")
    }
  }

  /** Validate that a SAM/BAM file has a single sample's reads.  */
  def validateHasSingleSample(sam: PathToBam): Unit = {
    val source = SamSource(sam)
    yieldAndThen(validateHasSingleSample(source))(source.safelyClose())
  }
}