ADAM_2.12: Core 0.29.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package util
  Definition Classes
    adam
- ADAMShell
- AttributeUtils
- FileExtensions
- GenomeFileReader
- IndexedFastaFile
- ParquetFileTraversable
- ParquetLogger
- PhredUtils
- ReferenceContigMap
- ReferenceContigMapSerializer
- ReferenceFile
- SequenceDictionaryReader
- TextRddWriter
- TwoBitFile
- TwoBitFileSerializer

c

org.bdgenomics.adam.util

# IndexedFastaFile 

###

#### case class IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ValidationStringency.STRICT) extends ReferenceFile with Logging with Product with Serializable

Loads and extracts sequences directly from indexed fasta or fa files. filePath requires fai index in the same directory with same naming convention.

filePath

  path to fasta or fa index

Linear Supertypes
Product, Equals, Logging, ReferenceFile, Serializable, Serializable, AnyRef, Any
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Ordering

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2. By Inheritance

Inherited

1. IndexedFastaFile
2. Product
3. Equals
4. Logging
5. ReferenceFile
6. Serializable
7. Serializable
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ValidationStringency.STRICT)

   filePath

     path to fasta or fa index

### 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.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  def clone(): AnyRef
   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @native() @throws( ... )
6.  def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
7.  def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
   Attributes
     protected
   Definition Classes
     Logging
8.  def debug(msg: ⇒ Any): Unit
   Attributes
     protected
   Definition Classes
     Logging
9.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
11.  def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
12.  def error(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
13.  def extract(region: ReferenceRegion): String

    Extracts base sequence from FastaSequenceIndex

    Extracts base sequence from FastaSequenceIndex

    region

      The desired ReferenceRegion to extract.

    returns

      The reference sequence at the desired locus.

    Definition Classes
      IndexedFastaFile → ReferenceFile
14.  val filePath: String
15.  def finalize(): Unit
    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )
16.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native()
17.  def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
18.  def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
19.  def info(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
20.  def isDebugEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
21.  def isErrorEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
22.  def isInfoEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
23.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
24.  def isTraceEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
25.  def isWarnEnabled: Boolean
    Attributes
      protected
    Definition Classes
      Logging
26.  def logger: Logger
    Attributes
      protected
    Definition Classes
      Logging
27.  def loggerName: String
    Attributes
      protected
    Definition Classes
      Logging
28.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
29.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
30.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
31.  val sc: SparkContext
32.  val sequences: SequenceDictionary
    Definition Classes
      IndexedFastaFile → ReferenceFile
33.  val stringency: ValidationStringency
34.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
35.  def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
36.  def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
37.  def trace(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging
38.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
39.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
40.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @throws( ... )
41.  def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
42.  def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
      protected
    Definition Classes
      Logging
43.  def warn(msg: ⇒ Any): Unit
    Attributes
      protected
    Definition Classes
      Logging

### Inherited from Product

### Inherited from Equals

### Inherited from Logging

### Inherited from ReferenceFile

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped