Package picard.illumina
Class ClusterDataToSamConverter
java.lang.Object
picard.illumina.ClusterDataToSamConverter
- 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
ConstructorsConstructorDescriptionClusterDataToSamConverter
(String runBarcode, Map<Integer, String> laneToReadGroup, ReadStructure readStructure, List<AdapterPair> adapters, picard.illumina.ClusterDataToSamConverter.PopulateBarcode barcodePopulationStrategy, boolean includeQualitiesWithBarcode) Constructor -
Method Summary
Modifier and TypeMethodDescriptionpicard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster
convertClusterToOutputRecord
(ClusterData cluster) Creates the SAMRecord for each read in the clusterwithMolecularIndexQualityTag
(String molecularIndexQualityTag) Sets the SAM tag to use to store the molecular index base qualities.withMolecularIndexTag
(String molecularIndexTag) Sets the SAM tag to use to store the molecular index bases.withTagPerMolecularIndex
(List<String> tagPerMolecularIndex) Sets the SAM tags to use to store the bases each molecular index.
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Constructor Details
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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 Details
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withMolecularIndexTag
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
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
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 interfaceBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>
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