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: AnyRef): Boolean

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

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

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4. #### final def ==(arg0: AnyRef): Boolean

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

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6. #### 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.

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

12. #### 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.

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

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

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

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

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      Logging

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

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

    Takes a sequence of Path objects (e.

    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.

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

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

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

22. #### def loadFastq(filePath1: String, filePath2Opt: Option[String], recordGroupOpt: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): RDD[AlignmentRecord]

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

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

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

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

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

28. #### 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

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

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

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

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

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

34. #### 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

49. #### def log: Logger

    Attributes
      protected
    Definition Classes
      Logging

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

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      Logging

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

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

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

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

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

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56. #### def logName: String

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

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

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

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

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      Logging

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

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

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

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64. #### val sc: SparkContext

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

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

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

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

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

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### Inherited from Logging

### Inherited from Serializable

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