Package htsjdk.samtools.filter
Class SecondaryAlignmentFilter
- java.lang.Object
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- htsjdk.samtools.filter.SecondaryAlignmentFilter
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- All Implemented Interfaces:
SamRecordFilter
- Direct Known Subclasses:
NotPrimaryAlignmentFilter
public class SecondaryAlignmentFilter extends Object implements SamRecordFilter
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
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Constructor Summary
Constructors Constructor Description SecondaryAlignmentFilter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
filterOut(SAMRecord record)
Returns true if the read is marked as secondary.boolean
filterOut(SAMRecord first, SAMRecord second)
Returns true if either read is marked as secondary.
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Method Detail
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filterOut
public boolean filterOut(SAMRecord record)
Returns true if the read is marked as secondary.- Specified by:
filterOut
in interfaceSamRecordFilter
- Parameters:
record
- the SAMRecord to evaluate- Returns:
- true if the SAMRecord matches the filter, otherwise false
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filterOut
public boolean filterOut(SAMRecord first, SAMRecord second)
Returns true if either read is marked as secondary.- Specified by:
filterOut
in interfaceSamRecordFilter
- Parameters:
first
- the first SAMRecord to evaluatesecond
- the second SAMRecord to evaluate- Returns:
- true if the pair of records matches filter, otherwise false
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