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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.

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  4. val arrayRegex: Regex
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  6. val attrRegex: Regex
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  8. 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.

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  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

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    Deprecated

    (Since version ) see corresponding Javadoc for more information.

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