org.bdgenomics.adam.rdd

# ADAMContext

#### class ADAMContext extends Serializable with Logging

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### Instance Constructors

1. #### new ADAMContext(sc: SparkContext)

### Value Members

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

   Definition Classes
     AnyRef → Any

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

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

   Definition Classes
     AnyRef → Any

4. #### def adamDictionaryLoad[T](filePath: String)(implicit ev1: (T) ⇒ SpecificRecord, ev2: Manifest[T]): SequenceDictionary

   This method should create a new SequenceDictionary from any parquet file which contains records that have the requisite reference{Name,Id,Length,Url} fields.

   This method should create a new SequenceDictionary from any parquet file which contains records that have the requisite reference{Name,Id,Length,Url} fields.

   (If the path is a BAM or SAM file, and the implicit type is an Read, then it just defaults to reading the SequenceDictionary out of the BAM header in the normal way.)

   T

     The type of records to return

   filePath

     The path to the input data

   returns

     A sequenceDictionary containing the names and indices of all the sequences to which the records in the corresponding file are aligned.

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

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

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     protected[java.lang]
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     @throws( ... )

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

   Definition Classes
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8. #### def equals(arg0: Any): Boolean

   Definition Classes
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9. #### def finalize(): Unit

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     protected[java.lang]
   Definition Classes
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   Annotations
     @throws( classOf[java.lang.Throwable] )

10. #### def findFiles(path: Path, regex: String): Seq[Path]

    Searches a path recursively, returning the names of all directories in the tree whose name matches the given regex.

    Searches a path recursively, returning the names of all directories in the tree whose name matches the given regex.

    path

      The path to begin the search at

    regex

      A regular expression

    returns

      A sequence of Path objects corresponding to the identified directories.

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

    Definition Classes
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12. #### def hashCode(): Int

    Definition Classes
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13. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
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14. #### def isTraceEnabled(): Boolean

    Attributes
      protected
    Definition Classes
      Logging

15. #### def loadAlignments(filePath: String, projection: Option[Schema] = None): RDD[AlignmentRecord]

16. #### def loadAlignmentsFromPaths(paths: Seq[Path]): RDD[AlignmentRecord]

    Takes a sequence of Path objects (e.g.

    Takes a sequence of Path objects (e.g. the return value of findFiles). Treats each path as corresponding to a Read set -- loads each Read set, converts each set to use the same SequenceDictionary, and returns the union of the RDDs.

    paths

      The locations of the parquet files to load

    returns

      a single RDD[Read] that contains the union of the AlignmentRecords in the argument paths.

17. #### def loadBED(filePath: String): RDD[Feature]

18. #### def loadBam(filePath: String): RDD[AlignmentRecord]

19. #### def loadFasta(filePath: String, fragmentLength: Long): RDD[NucleotideContigFragment]

20. #### def loadFeatures(filePath: String, projection: Option[Schema] = None): RDD[Feature]

21. #### def loadGTF(filePath: String): RDD[Feature]

22. #### def loadGenes(filePath: String, projection: Option[Schema] = None): RDD[Gene]

23. #### def loadGenotypes(filePath: String, projection: Option[Schema] = None, sd: Option[SequenceDictionary] = None): RDD[Genotype]

24. #### def loadIndexedBam(filePath: String, viewRegion: ReferenceRegion): RDD[AlignmentRecord]

    Functions like loadBam, but uses bam index files to look at fewer blocks, and only returns records within a specified ReferenceRegion.

    Functions like loadBam, but uses bam index files to look at fewer blocks, and only returns records within a specified ReferenceRegion. Bam index file required.

    filePath

      The path to the input data. Currently this path must correspond to a single Bam file. The bam index file associated needs to have the same name.

    viewRegion

      The ReferenceRegion we are filtering on

25. #### def loadInterleavedFastq(filePath: String): RDD[AlignmentRecord]

26. #### def loadIntervalList(filePath: String): RDD[Feature]

27. #### def loadNarrowPeak(filePath: String): RDD[Feature]

28. #### def loadParquet[T](filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None)(implicit ev1: (T) ⇒ SpecificRecord, ev2: Manifest[T]): RDD[T]

    This method will create a new RDD.

    This method will create a new RDD.

    T

      The type of records to return

    filePath

      The path to the input data

    predicate

      An optional pushdown predicate to use when reading the data

    projection

      An option projection schema to use when reading the data

    returns

      An RDD with records of the specified type

29. #### def loadParquetAlignments(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[AlignmentRecord]

30. #### def loadParquetFeatures(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[Feature]

31. #### def loadParquetFragments(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[NucleotideContigFragment]

32. #### def loadParquetGenotypes(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[Genotype]

33. #### def loadParquetVariantAnnotations(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[DatabaseVariantAnnotation]

34. #### def loadParquetVariants(filePath: String, predicate: Option[FilterPredicate] = None, projection: Option[Schema] = None): RDD[Variant]

35. #### def loadSequence(filePath: String, projection: Option[Schema] = None, fragmentLength: Long = 10000): RDD[NucleotideContigFragment]

36. #### def loadUnpairedFastq(filePath: String): RDD[AlignmentRecord]

37. #### def loadVariantAnnotations(filePath: String, projection: Option[Schema] = None, sd: Option[SequenceDictionary] = None): RDD[DatabaseVariantAnnotation]

38. #### def loadVariants(filePath: String, projection: Option[Schema] = None, sd: Option[SequenceDictionary] = None): RDD[Variant]

39. #### def loadVcf(filePath: String, sd: Option[SequenceDictionary]): RDD[VariantContext]

40. #### def loadVcfAnnotations(filePath: String, sd: Option[SequenceDictionary] = None): RDD[DatabaseVariantAnnotation]

41. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

42. #### def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

43. #### def logDebug(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

44. #### def logError(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

45. #### def logError(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

46. #### def logInfo(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

47. #### def logInfo(msg: ⇒ String): Unit

    Attributes
      protected
    Definition Classes
      Logging

48. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

49. #### def logTrace(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
    Definition Classes
      Logging

50. #### def logTrace(msg: ⇒ String): Unit

    Attributes
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    Definition Classes
      Logging

51. #### def logWarning(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
      protected
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      Logging

52. #### def logWarning(msg: ⇒ String): Unit

    Attributes
      protected
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      Logging

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

    Definition Classes
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54. #### final def notify(): Unit

    Definition Classes
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55. #### final def notifyAll(): Unit

    Definition Classes
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56. #### val sc: SparkContext

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

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

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

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      @throws( ... )

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

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      @throws( ... )

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

    Definition Classes
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      @throws( ... )

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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