org.bdgenomics.adam.rdd

# ADAMContext

#### class ADAMContext extends Serializable with Logging

Linear Supertypes
Logging, Serializable, Serializable, AnyRef, Any
Ordering

1. Alphabetic
2. By inheritance

Inherited

1. ADAMContext
2. Logging
3. Serializable
4. Serializable
5. AnyRef
6. Any

1. Hide All
2. Show all

Learn more about member selection
Visibility

1. Public
2. All

### 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
     AnyRef → Any

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

   Definition Classes
     Any

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

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

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

   Definition Classes
     AnyRef

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

   Definition Classes
     AnyRef → Any

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

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   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
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      Any

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

    Attributes
      protected
    Definition Classes
      Logging

15. #### def loadAlignments(filePath: String, projection: Option[Schema] = None, filePath2Opt: Option[String] = None, recordGroupOpt: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): 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 loadFastq(filePath1: String, filePath2Opt: Option[String], recordGroupOpt: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): RDD[AlignmentRecord]

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

22. #### def loadFragments(filePath: String): RDD[Fragment]

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

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

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

26. #### 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

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

28. #### def loadInterleavedFastqAsFragments(filePath: String): RDD[Fragment]

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

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

31. #### def loadPairedFastq(filePath1: String, filePath2: String, recordGroupOpt: Option[String], stringency: ValidationStringency): RDD[AlignmentRecord]

32. #### 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

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

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

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

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

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

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

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

40. #### def loadReferenceFile(filePath: String, fragmentLength: Long): ReferenceFile

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

42. #### def loadUnpairedFastq(filePath: String, recordGroupOpt: Option[String] = None, setFirstOfPair: Boolean = false, setSecondOfPair: Boolean = false, stringency: ValidationStringency = ValidationStringency.STRICT): RDD[AlignmentRecord]

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

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

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

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

47. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

54. #### def logName: String

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Attributes
      protected
    Definition Classes
      Logging

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

62. #### val sc: SparkContext

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Logging

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped