Type Members

1.  final case class SamMapping (record: SAMRecord, firstOfPairStrandOnTranscript: Orientation) extends GenericFeature with Product with Serializable

   A Feature representing a mapped SAM record.

   A Feature representing a mapped SAM record.

   The Blocks of this SamMapping are the aligned blocks of the SAM record translated to zero-based half-open intervals.

   If the sequencing library is strand specific, the Orientation of this Feature is the transcription strand of the entire fragment the record came from. For example, if the reads are unpaired and strand-specific, and always map to the transcription strand for this library, then this SamMapping will have Orientation Plus for a read mapped to the plus strand or Minus for a read mapped to the minus strand. If the reads are paired and read 1 always gives the transcription strand for this library, and we have a pair of records with read 1 mapped to the plus strand and read 2 mapped to the minus strand, then the entire fragment was transcribed from the plus strand, so the Orientation of both SamMappings is Plus.

   If the library is not RNA-seq or is not strand specific, the Orientation is Unstranded.

   record

   The SAM record

   firstOfPairStrandOnTranscript

   Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.

2.  class SamReader extends AnyRef

   A wrapper around an htsjdk.samtools.SamReader.