org.bdgenomics.adam.util

# AttributeUtils

#### object AttributeUtils

AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.

Linear Supertypes
AnyRef, Any
Ordering

1. Alphabetic
2. By inheritance

Inherited

1. AttributeUtils
2. AnyRef
3. Any

1. Hide All
2. Show all

Learn more about member selection
Visibility

1. Public
2. All

### 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. #### val attrRegex: RegExp

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

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

7. #### def convertSAMTagAndValue(attr: SAMTagAndValue): Attribute

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

   Definition Classes
     AnyRef

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

   Definition Classes
     AnyRef → Any

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

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

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

17. #### def parseAttribute(encoded: String): Attribute

    Extract the Attribute value from the corresponding String fragment stored in the Read.attributes field.

    Extract the Attribute value from the corresponding String fragment stored in the Read.attributes field.

    encoded

      A three-part ':'-separated string, containing [attrTuple]:[type]:[value]

    returns

      An Attribute value which has the three, extracted and correctly-typed parts of the encoded argument.

    Exceptions thrown
      IllegalArgumentException

      if the encoded string doesn't conform to the required regular expression ([A-Z]{2}:[AifZHB]:[\t]+)

18. #### def parseAttributes(tagStrings: String): Seq[Attribute]

    Parses a tab-separated string of attributes (tag:type:value) into a Seq of Attribute values.

    Parses a tab-separated string of attributes (tag:type:value) into a Seq of Attribute values.

    tagStrings

      The String to be parsed

    returns

      The parsed Attributes

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from AnyRef

### Inherited from Any

### Ungrouped