picard.filter

Class CountingFilter

java.lang.Object

picard.filter.CountingFilter

All Implemented Interfaces:

htsjdk.samtools.filter.SamRecordFilter

Direct Known Subclasses:

CountingDuplicateFilter, CountingMapQFilter, CountingPairedFilter

public abstract class CountingFilter
extends java.lang.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.

Constructor Summary

Constructors

Constructor and Description
CountingFilter()

Method Summary

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CountingFilter

public CountingFilter()

Method Detail

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 interface htsjdk.samtools.filter.SamRecordFilter

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 interface htsjdk.samtools.filter.SamRecordFilter