Package picard.filter
Class CountingFilter
- java.lang.Object
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- picard.filter.CountingFilter
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- All Implemented Interfaces:
htsjdk.samtools.filter.SamRecordFilter
- Direct Known Subclasses:
CountingAdapterFilter
,CountingDuplicateFilter
,CountingMapQFilter
,CountingPairedFilter
public abstract class CountingFilter extends Object implements htsjdk.samtools.filter.SamRecordFilter
A SamRecordFilter that counts the number of bases in the reads which it filters out. Abstract and designed to be sub-classed to implement the desired filter. The filterOut method will count the number of records and bases that would be filtered out using the result of the reallyFilterOut method.
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Constructor Summary
Constructors Constructor Description CountingFilter()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description boolean
filterOut(htsjdk.samtools.SAMRecord record)
boolean
filterOut(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second)
long
getFilteredBases()
Gets the number of bases that have been filtered out thus far.long
getFilteredRecords()
Gets the number of records that have been filtered out thus far.abstract boolean
reallyFilterOut(htsjdk.samtools.SAMRecord record)
Return true if we are to filter this record out, false otherwise.
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Method Detail
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getFilteredRecords
public long getFilteredRecords()
Gets the number of records that have been filtered out thus far.
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getFilteredBases
public long getFilteredBases()
Gets the number of bases that have been filtered out thus far.
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filterOut
public final boolean filterOut(htsjdk.samtools.SAMRecord record)
- Specified by:
filterOut
in interfacehtsjdk.samtools.filter.SamRecordFilter
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reallyFilterOut
public abstract boolean reallyFilterOut(htsjdk.samtools.SAMRecord record)
Return true if we are to filter this record out, false otherwise.
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filterOut
public boolean filterOut(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second)
- Specified by:
filterOut
in interfacehtsjdk.samtools.filter.SamRecordFilter
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