Package htsjdk.samtools.filter
Class OverclippedReadFilter
java.lang.Object
htsjdk.samtools.filter.OverclippedReadFilter
- All Implemented Interfaces:
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
ConstructorDescriptionOverclippedReadFilter
(int unclippedBasesThreshold, boolean filterSingleEndClips) -
Method Summary
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Constructor Details
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OverclippedReadFilter
public OverclippedReadFilter(int unclippedBasesThreshold, boolean filterSingleEndClips)
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Method Details
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filterOut
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
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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