Package htsjdk.samtools.filter
Class OverclippedReadFilter
- java.lang.Object
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- htsjdk.samtools.filter.OverclippedReadFilter
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- All Implemented Interfaces:
SamRecordFilter
public class OverclippedReadFilter extends Object implements SamRecordFilter
Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g. bacterial contamination. Based on GATK's OverclippedReadFilter.
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Constructor Summary
Constructors Constructor Description OverclippedReadFilter(int unclippedBasesThreshold, boolean filterSingleEndClips)
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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 SAMRecords 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)
Description copied from interface:SamRecordFilter
Determines whether a pair of SAMRecords matches this filter- 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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