Package htsjdk.samtools.filter
Class SecondaryOrSupplementaryFilter
- java.lang.Object
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- htsjdk.samtools.filter.SecondaryOrSupplementaryFilter
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- All Implemented Interfaces:
SamRecordFilter
public class SecondaryOrSupplementaryFilter extends Object implements SamRecordFilter
Filter out SAMRecords with Secondary or Supplementary flag set This class should be viewed as a replacement forNotPrimarySkippingIterator
, in that we did not want to change the functionality of NPSI to no longer match its name $Id$
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Constructor Summary
Constructors Constructor Description SecondaryOrSupplementaryFilter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
filterOut(SAMRecord record)
Determines whether a SAMRecord matches this filterboolean
filterOut(SAMRecord first, SAMRecord second)
Determines whether a pair of SAMRecord matches this filter
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Method Detail
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filterOut
public boolean filterOut(SAMRecord record)
Description copied from interface:SamRecordFilter
Determines whether a SAMRecord matches this filter- 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)
Determines whether a pair 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 the SAMRecords matches the filter, otherwise false
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