org.bdgenomics.adam.rdd.fragment
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.
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).
A genomic dataset that supports Datasets of Fragments.
A genomic dataset that supports Datasets of Fragments.
The underlying Dataset of Fragment data.
The genomic sequences this data was aligned to, if any.
The read groups these Fragments came from.
The processing steps that have been applied to this data.
A new FragmentDataset.
A genomic dataset that supports Datasets of Fragments.
A genomic dataset that supports Datasets of Fragments.
The underlying Dataset of Fragment data.
A new FragmentDataset.
Builds a FragmentDataset without a partition map.
Builds a FragmentDataset without a partition map.
The underlying Fragment RDD.
The sequence dictionary for the genomic dataset.
The read group dictionary for the genomic dataset.
The processing steps that have been applied to this data.
A new FragmentDataset.
Helper singleton object for building FragmentDatasets.