object AlignmentDataset extends Serializable
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val
WRITE_ORIGINAL_QUALITY_SCORES: String
Hadoop configuration path to check for a boolean value indicating whether the current or original read quality scores should be written.
Hadoop configuration path to check for a boolean value indicating whether the current or original read quality scores should be written. True indicates to write the original quality scores. The default is false.
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val
WRITE_SUFFIXES: String
Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair.
Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair. Default is false (no suffixes).
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def
apply(ds: Dataset[Alignment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentDataset
Builds an AlignmentDataset without a partition map from a Dataset.
Builds an AlignmentDataset without a partition map from a Dataset.
- ds
The underlying Alignment Dataset.
- sequences
The sequence dictionary for the genomic dataset.
- readGroups
The read group dictionary for the genomic dataset.
- processingSteps
The processing steps for the genomic dataset.
- returns
A new AlignmentDataset.
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def
apply(ds: Dataset[Alignment]): AlignmentDataset
Builds an AlignmentDataset without a partition map from a Dataset.
Builds an AlignmentDataset without a partition map from a Dataset.
- ds
The underlying Alignment Dataset.
- returns
A new AlignmentDataset.
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def
apply(rdd: RDD[Alignment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentDataset
Builds an AlignmentDataset without a partition map from an RDD.
Builds an AlignmentDataset without a partition map from an RDD.
- rdd
The underlying Alignment RDD.
- sequences
The sequence dictionary for the genomic dataset.
- readGroups
The read group dictionary for the genomic dataset.
- processingSteps
The processing steps for the genomic dataset.
- returns
A new AlignmentDataset.
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def
unaligned(rdd: RDD[Alignment]): AlignmentDataset
Builds an AlignmentDataset for unaligned reads.
Builds an AlignmentDataset for unaligned reads.
- rdd
The underlying Alignment RDD.
- returns
A new AlignmentDataset.
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