Package picard.filter
Class CountingFilter
java.lang.Object
picard.filter.CountingFilter
- 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 -
Method Summary
Modifier and TypeMethodDescriptionfinal boolean
filterOut
(htsjdk.samtools.SAMRecord record) boolean
filterOut
(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second) long
Gets the number of bases that have been filtered out thus far.long
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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Constructor Details
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CountingFilter
public CountingFilter()
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Method Details
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getFilteredRecords
public long getFilteredRecords()Gets the number of records that have been filtered out thus far. -
getFilteredBases
public long getFilteredBases()Gets the number of bases that have been filtered out thus far. -
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. -
filterOut
public boolean filterOut(htsjdk.samtools.SAMRecord first, htsjdk.samtools.SAMRecord second) - Specified by:
filterOut
in interfacehtsjdk.samtools.filter.SamRecordFilter
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