org.bdgenomics.adam.apis.java

# JavaAlignmentRecordRDD

#### class JavaAlignmentRecordRDD extends Serializable

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### Instance Constructors

1. #### new JavaAlignmentRecordRDD(jrdd: JavaRDD[AlignmentRecord], sd: SequenceDictionary, rgd: RecordGroupDictionary)

### Value Members

1. #### final def !=(arg0: Any): Boolean

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2. #### final def ##(): Int

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3. #### final def ==(arg0: Any): Boolean

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4. #### def adamSAMSave(filePath: String, asSam: Boolean, asSingleFile: Boolean, isSorted: Boolean): Unit

   Saves this RDD to disk as a SAM/BAM file.

   Saves this RDD to disk as a SAM/BAM file.

   filePath

     Path to save the file at.

   asSam

     If true, saves as SAM. If false, saves as BAM.

   asSingleFile

     If true, saves output as a single file.

   isSorted

     If the output is sorted, this will modify the header.

5. #### def adamSave(filePath: String): Unit

   Saves this RDD to disk as a Parquet file.

   Saves this RDD to disk as a Parquet file.

   filePath

     Path to save the file at.

6. #### def adamSave(filePath: String, blockSize: Integer, pageSize: Integer, compressCodec: CompressionCodecName, disableDictionaryEncoding: Boolean): Unit

   Saves this RDD to disk as a Parquet file.

   Saves this RDD to disk as a Parquet file.

   filePath

     Path to save the file at.

   blockSize

     Size per block.

   pageSize

     Size per page.

   compressCodec

     Name of the compression codec to use.

   disableDictionaryEncoding

     Whether or not to disable bit-packing.

7. #### final def asInstanceOf[T0]: T0

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8. #### def clone(): AnyRef

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9. #### final def eq(arg0: AnyRef): Boolean

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10. #### def equals(arg0: Any): Boolean

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11. #### def finalize(): Unit

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12. #### final def getClass(): Class[_]

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13. #### def hashCode(): Int

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14. #### final def isInstanceOf[T0]: Boolean

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15. #### val jrdd: JavaRDD[AlignmentRecord]

16. #### final def ne(arg0: AnyRef): Boolean

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17. #### final def notify(): Unit

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18. #### final def notifyAll(): Unit

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19. #### val rgd: RecordGroupDictionary

20. #### val sd: SequenceDictionary

21. #### final def synchronized[T0](arg0: ⇒ T0): T0

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22. #### def toString(): String

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23. #### final def wait(): Unit

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24. #### final def wait(arg0: Long, arg1: Int): Unit

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25. #### final def wait(arg0: Long): Unit

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