Package htsjdk.samtools.filter
Class TagFilter
java.lang.Object
htsjdk.samtools.filter.TagFilter
- All Implemented Interfaces:
SamRecordFilter
Filter class for matching tag attributes in SAMRecords
$Id$
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Constructor Summary
ConstructorsConstructorDescriptionConstructor for a single valueConstructor for a single valueConstructor for multiple valuesConstructor for multiple values -
Method Summary
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Constructor Details
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TagFilter
Constructor for a single value- Parameters:
tag
- the key of the tag to matchvalue
- the value to match
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TagFilter
Constructor for multiple values- Parameters:
tag
- the key of the tag to matchvalues
- the matching values
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TagFilter
Constructor for a single value- Parameters:
tag
- the key of the tag to matchvalue
- the value to matchincludeReads
- whether to include or not include reads that match filter
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TagFilter
Constructor for multiple values- Parameters:
tag
- the key of the tag to matchvalues
- the matching valuesincludeReads
- whether to include or not include reads that match filter
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Method Details
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filterOut
Determines whether a SAMRecord matches this filter- Specified by:
filterOut
in interfaceSamRecordFilter
- Parameters:
record
- the SAMRecord to evaluate- Returns:
- the XOR of SAMRecord matches the filter and includeReads.
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filterOut
Determines whether a paired of SAMRecord matches this filter- Specified by:
filterOut
in interfaceSamRecordFilter
- Parameters:
first
- the first SAMRecord to evaluatesecond
- the second SAMRecord to evaluate- Returns:
- true if includeReads is true and neither SAMRecord matches filter true if includeReads is false and both SAMRecords match filter otherwise false
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