Package picard.fastq
Class IlluminaReadNameEncoder
java.lang.Object
picard.fastq.IlluminaReadNameEncoder
- All Implemented Interfaces:
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 -
Method Summary
Modifier and TypeMethodDescriptiongenerateReadName
(ClusterData cluster, Integer pairNumber) Generates a read name string for the provided cluster.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 Details
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IlluminaReadNameEncoder
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Method Details
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generateReadName
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
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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