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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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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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]+)
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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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