picard.illumina

Class ClusterDataToSamConverter

java.lang.Object

picard.illumina.ClusterDataToSamConverter

All Implemented Interfaces:

IlluminaBasecallsConverter.ClusterDataConverter<picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster>

public class ClusterDataToSamConverter
extends java.lang.Object
implements IlluminaBasecallsConverter.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.

Constructor Summary

Constructors

Constructor and Description
ClusterDataToSamConverter(java.lang.String runBarcode, java.lang.String readGroupId, ReadStructure readStructure, java.util.List<IlluminaUtil.IlluminaAdapterPair> adapters) Constructor

Method Summary

Modifier and Type	Method and Description
picard.illumina.IlluminaBasecallsToSam.SAMRecordsForCluster	convertClusterToOutputRecord(ClusterData cluster) Creates the SAMRecord for each read in the cluster

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ClusterDataToSamConverter

public ClusterDataToSamConverter(java.lang.String runBarcode,
                                 java.lang.String readGroupId,
                                 ReadStructure readStructure,
                                 java.util.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

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>