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: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. val arrayRegex: Regex

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. val attrRegex: Regex

  9. def clone(): AnyRef

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

  10. def convertSAMTagAndValue(attr: SAMTagAndValue): Attribute

    Converts an htsjdk SAM Tag/Value into an ADAM attribute.

    Converts an htsjdk SAM Tag/Value into an ADAM attribute.

    attr

    htsjdk tag/value pair containing a tag value with a known type.

    returns

    Returns an Attribute instance.

  11. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  13. def finalize(): Unit

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

  14. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  15. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  18. final def notify(): Unit

    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  20. def parseAttribute(encoded: String): Attribute

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

    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]+)

  21. 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

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

    Definition Classes
    AnyRef

  23. def toString(): String

    Definition Classes
    AnyRef → Any

  24. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  26. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped