Package picard.fastq
Class IlluminaReadNameEncoder
- java.lang.Object
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- picard.fastq.IlluminaReadNameEncoder
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- All Implemented Interfaces:
ReadNameEncoder
public class IlluminaReadNameEncoder extends Object implements ReadNameEncoder
A read name encoder following the encoding initially produced by picard fastq writers. Illumina sequence identifiers almost describes the format used here, except instead of an instrument name, we write the run barcode.
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Constructor Summary
Constructors Constructor Description IlluminaReadNameEncoder(String runBarcode)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
generateReadName(ClusterData cluster, Integer pairNumber)
Generates a read name string for the provided cluster.String
generateShortName(ClusterData cluster)
Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
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Constructor Detail
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IlluminaReadNameEncoder
public IlluminaReadNameEncoder(String runBarcode)
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Method Detail
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generateReadName
public String generateReadName(ClusterData cluster, Integer pairNumber)
Description copied from interface:ReadNameEncoder
Generates a read name string for the provided cluster.- Specified by:
generateReadName
in interfaceReadNameEncoder
- Parameters:
cluster
- The cluster whose reads are having its name generatedpairNumber
- 1 if this is the first of the pair, 2 if it is the second, or null if this not a paired read.- Returns:
- The read name
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generateShortName
public String generateShortName(ClusterData cluster)
Description copied from interface:ReadNameEncoder
Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.- Specified by:
generateShortName
in interfaceReadNameEncoder
- Parameters:
cluster
- The cluster to generate the short read name from- Returns:
- The short read name
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