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.

Author:

jburke@broadinstitute.org

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
ClusterDataToSamConverter	withMolecularIndexQualityTag(java.lang.String molecularIndexQualityTag) Sets the SAM tag to use to store the molecular index base qualities.
ClusterDataToSamConverter	withMolecularIndexTag(java.lang.String molecularIndexTag) Sets the SAM tag to use to store the molecular index bases.
ClusterDataToSamConverter	withTagPerMolecularIndex(java.util.List<java.lang.String> tagPerMolecularIndex) Sets the SAM tags to use to store the bases each molecular index.

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

withMolecularIndexTag

public ClusterDataToSamConverter withMolecularIndexTag(java.lang.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(java.lang.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(java.util.List<java.lang.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>