CountingFilter (picard 2.24.1 API)

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.

Constructor Summary

Constructors
Constructor Description

CountingFilter()

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.

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