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

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

    Definition Classes
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  4. final def ==(arg0: AnyRef): Boolean

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

    Attributes
    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[_]

    Definition Classes
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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

    Attributes
    protected
    Definition Classes
    Logging
  17. def loadAlignments(filePath: String, projection: Option[Schema] = None): 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 loadFeatures(filePath: String, projection: Option[Schema] = None): RDD[Feature]

  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 loadInterleavedFastq(filePath: String): RDD[AlignmentRecord]

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

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

  29. 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

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

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

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

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

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

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

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

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

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

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

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

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

  42. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging
  43. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

    Attributes
    protected
    Definition Classes
    Logging
  44. def logDebug(msg: ⇒ String): Unit

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    Logging
  45. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    protected
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  46. def logError(msg: ⇒ String): Unit

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

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  48. def logInfo(msg: ⇒ String): Unit

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  49. def logName: String

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

    Attributes
    protected
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  51. def logTrace(msg: ⇒ String): Unit

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

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    protected
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  53. def logWarning(msg: ⇒ String): Unit

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  54. final def ne(arg0: AnyRef): Boolean

    Definition Classes
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  55. final def notify(): Unit

    Definition Classes
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  56. final def notifyAll(): Unit

    Definition Classes
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  57. val sc: SparkContext

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

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  59. def toString(): String

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  60. final def wait(): Unit

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    @throws( ... )
  61. final def wait(arg0: Long, arg1: Int): Unit

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    @throws( ... )
  62. final def wait(arg0: Long): Unit

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Inherited from Logging

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