Constructor Detail

• ClusterDataToSamConverter

  public ClusterDataToSamConverter(String runBarcode,
                                   String readGroupId,
                                   ReadStructure readStructure,
                                   List<IlluminaUtil.IlluminaAdapterPair> adapters)

  Constructor

  Parameters:

  runBarcode - Used to construct read names.

  readGroupId - If non-null, set RG attribute on SAMRecord to this.

  readStructure - The expected structure (number of reads and indexes, and their length) in the read.

  adapters - The list of adapters to check for in the read

Method Detail

• withMolecularIndexTag

  public ClusterDataToSamConverter withMolecularIndexTag(String molecularIndexTag)

  Sets the SAM tag to use to store the molecular index bases. If multiple molecular indexes exist, it will concatenate them and store them in this tag.

• withMolecularIndexQualityTag

  public ClusterDataToSamConverter withMolecularIndexQualityTag(String molecularIndexQualityTag)

  Sets the SAM tag to use to store the molecular index base qualities. If multiple molecular indexes exist, it will concatenate them and store them in this tag.

• withTagPerMolecularIndex

  public ClusterDataToSamConverter withTagPerMolecularIndex(List<String> tagPerMolecularIndex)

  Sets the SAM tags to use to store the bases each molecular index. This will only be used if there are more than one molecular index. If fewer tags are given than molecular indexes found, then the remaining molecular indexes will be concatenated and stored in the last tag. If more tags are provided than molecular indexes found, the additional tags will not be used.

• convertClusterToOutputRecord

  public picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster convertClusterToOutputRecord(ClusterData cluster)

  Creates the SAMRecord for each read in the cluster

  Specified by:

  convertClusterToOutputRecord in interface IlluminaBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>