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org.bdgenomics.adam.util

AttributeUtils

Related Doc: package util

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object AttributeUtils

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

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

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  2. final def ##(): Int

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

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  4. val arrayRegex: Regex

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  5. final def asInstanceOf[T0]: T0

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  6. val attrRegex: Regex

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  8. def convertSAMTagAndValue(attr: SAMTagAndValue): Attribute

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    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.

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

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

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  16. final def notify(): Unit

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  17. final def notifyAll(): Unit

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  18. def parseAttribute(encoded: String): Attribute

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    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]+)

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

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    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

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

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  21. def toString(): String

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

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