Package picard.illumina
Class ClusterDataToSamConverter
- java.lang.Object
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- picard.illumina.ClusterDataToSamConverter
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- All Implemented Interfaces:
BasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>
public class ClusterDataToSamConverter extends Object implements BasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence. There is one converter per IlluminaBasecallsToSam run, and all the TileProcessors use the same converter.
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Constructor Summary
Constructors Constructor Description ClusterDataToSamConverter(String runBarcode, Map<Integer,String> laneToReadGroup, ReadStructure readStructure, List<AdapterPair> adapters, picard.illumina.ClusterDataToSamConverter.PopulateBarcode barcodePopulationStrategy, boolean includeQualitiesWithBarcode)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster
convertClusterToOutputRecord(ClusterData cluster)
Creates the SAMRecord for each read in the clusterClusterDataToSamConverter
withMolecularIndexQualityTag(String molecularIndexQualityTag)
Sets the SAM tag to use to store the molecular index base qualities.ClusterDataToSamConverter
withMolecularIndexTag(String molecularIndexTag)
Sets the SAM tag to use to store the molecular index bases.ClusterDataToSamConverter
withTagPerMolecularIndex(List<String> tagPerMolecularIndex)
Sets the SAM tags to use to store the bases each molecular index.
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Constructor Detail
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ClusterDataToSamConverter
public ClusterDataToSamConverter(String runBarcode, Map<Integer,String> laneToReadGroup, ReadStructure readStructure, List<AdapterPair> adapters, picard.illumina.ClusterDataToSamConverter.PopulateBarcode barcodePopulationStrategy, boolean includeQualitiesWithBarcode)
Constructor- Parameters:
runBarcode
- Used to construct read names.laneToReadGroup
- 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 readbarcodePopulationStrategy
- When to populate BC tag?
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Method Detail
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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.
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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.
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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.
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convertClusterToOutputRecord
public picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster convertClusterToOutputRecord(ClusterData cluster)
Creates the SAMRecord for each read in the cluster- Specified by:
convertClusterToOutputRecord
in interfaceBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>
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