public class ClusterDataToSamConverter extends Object implements IlluminaBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>
Constructor and Description |
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ClusterDataToSamConverter(String runBarcode,
String readGroupId,
ReadStructure readStructure,
List<IlluminaUtil.IlluminaAdapterPair> adapters)
Constructor
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Modifier and Type | Method and Description |
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picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster |
convertClusterToOutputRecord(ClusterData cluster)
Creates the SAMRecord for each read in the cluster
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ClusterDataToSamConverter |
withMolecularIndexQualityTag(String molecularIndexQualityTag)
Sets the SAM tag to use to store the molecular index base qualities.
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ClusterDataToSamConverter |
withMolecularIndexTag(String molecularIndexTag)
Sets the SAM tag to use to store the molecular index bases.
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ClusterDataToSamConverter |
withTagPerMolecularIndex(List<String> tagPerMolecularIndex)
Sets the SAM tags to use to store the bases each molecular index.
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public ClusterDataToSamConverter(String runBarcode, String readGroupId, ReadStructure readStructure, List<IlluminaUtil.IlluminaAdapterPair> adapters)
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 readpublic ClusterDataToSamConverter withMolecularIndexTag(String molecularIndexTag)
public ClusterDataToSamConverter withMolecularIndexQualityTag(String molecularIndexQualityTag)
public ClusterDataToSamConverter withTagPerMolecularIndex(List<String> tagPerMolecularIndex)
public picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster convertClusterToOutputRecord(ClusterData cluster)
convertClusterToOutputRecord
in interface IlluminaBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>