org.bdgenomics.adam.rdd.fragment

# FragmentRDD

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Related Docs: class FragmentRDD | package fragment

#### object FragmentRDD extends Serializable

Helper singleton object for building FragmentRDDs.

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4. #### val WRITE_ORIGINAL_QUALITIES: String

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written.

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written. True indicates to write the original qualities. The default is false.

5. #### 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).

6. #### def apply(ds: Dataset[Fragment], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentRDD

   A genomic RDD that supports Datasets of Fragments.

   A genomic RDD that supports Datasets of Fragments.

   ds

     The underlying Dataset of Fragment data.

   sequences

     The genomic sequences this data was aligned to, if any.

   recordGroups

     The record groups these Fragments came from.

   processingSteps

     The processing steps that have been applied to this data.

   returns

     A new FragmentRDD.

7. #### def apply(rdd: RDD[Fragment], sequences: SequenceDictionary, recordGroupDictionary: RecordGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentRDD

   Builds a FragmentRDD without a partition map.

   Builds a FragmentRDD without a partition map.

   rdd

     The underlying Franment RDD.

   sequences

     The sequence dictionary for the RDD.

   recordGroupDictionary

     The record group dictionary for the RDD.

   processingSteps

     The processing steps that have been applied to this data.

   returns

     A new FragmentRDD.

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