object FragmentDataset
Helper singleton object for building FragmentDatasets.
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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[Fragment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset
A genomic dataset that supports Datasets of Fragments.
A genomic dataset that supports Datasets of Fragments.
- ds
The underlying Dataset of Fragment data.
- sequences
The genomic sequences this data was aligned to, if any.
- readGroups
The read groups these Fragments came from.
- processingSteps
The processing steps that have been applied to this data.
- returns
A new FragmentDataset.
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def
apply(ds: Dataset[Fragment]): FragmentDataset
A genomic dataset that supports Datasets of Fragments.
A genomic dataset that supports Datasets of Fragments.
- ds
The underlying Dataset of Fragment data.
- returns
A new FragmentDataset.
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def
apply(rdd: RDD[Fragment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset
Builds a FragmentDataset without a partition map.
Builds a FragmentDataset without a partition map.
- rdd
The underlying Fragment RDD.
- sequences
The sequence dictionary for the genomic dataset.
- readGroups
The read group dictionary for the genomic dataset.
- processingSteps
The processing steps that have been applied to this data.
- returns
A new FragmentDataset.
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