SAMRecordDuplicateComparator (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.SAMRecordDuplicateComparator

All Implemented Interfaces:

SAMRecordComparator, Serializable, Comparator<SAMRecord>
```
public class SAMRecordDuplicateComparator
extends Object
implements SAMRecordComparator, Serializable
```
Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates). There are three orderings provided by this comparator: compare, duplicateSetCompare, and fileOrderCompare. Specify the headers when constructing this comparator if you would like to consider the library as the major sort key. The records being compared must also have non-null SAMFileHeaders.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

SAMRecordDuplicateComparator()

SAMRecordDuplicateComparator(List<SAMFileHeader> headers)

Constructors
Constructor	Description
`SAMRecordDuplicateComparator()`
`SAMRecordDuplicateComparator(List<SAMFileHeader> headers)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`compare(SAMRecord samRecord1, SAMRecord samRecord2)`	Most stringent comparison.
`int`	`duplicateSetCompare(SAMRecord samRecord1, SAMRecord samRecord2)`	Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary.
`int`	`fileOrderCompare(SAMRecord samRecord1, SAMRecord samRecord2)`	Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.
`void`	`setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy)`

Methods inherited from interface java.util.Comparator
equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SAMRecordDuplicateComparator
```
public SAMRecordDuplicateComparator()
```
  - SAMRecordDuplicateComparator
```
public SAMRecordDuplicateComparator(List<SAMFileHeader> headers)
```
- Method Detail
  - setScoringStrategy
```
public void setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy)
```
  - compare
```
public int compare(SAMRecord samRecord1,
                   SAMRecord samRecord2)
```
    Most stringent comparison. Two records are compared based on if they are duplicates of each other, and then based on if they should be prioritized for being the most "representative". Typically, the representative is the record in the SAM file that is *not* marked as a duplicate within a set of duplicates. Compare by file order, then duplicate scoring strategy, read name. If both reads are paired and both ends mapped, always prefer the first end over the second end. This is needed to properly choose the first end for optical duplicate identification when both ends are mapped to the same position etc.
    
    Specified by:
    
    compare in interface Comparator<SAMRecord>
  - duplicateSetCompare
```
public int duplicateSetCompare(SAMRecord samRecord1,
                               SAMRecord samRecord2)
```
    Less stringent than compare, such that two records are equal enough such that their ordering within their duplicate set would be arbitrary. Major difference between this and fileOrderCompare is how we compare the orientation byte. Here we want: F == FR, F == FF R == RF, R == RR
  - fileOrderCompare
```
public int fileOrderCompare(SAMRecord samRecord1,
                            SAMRecord samRecord2)
```
    Less stringent than duplicateSetCompare, such that two records are equal enough such that their ordering in a sorted SAM file would be arbitrary.
    
    Specified by:
    
    fileOrderCompare in interface SAMRecordComparator
    
    Returns:
    
    negative if samRecord1 < samRecord2, 0 if equal, else positive

Class SAMRecordDuplicateComparator

Constructor Summary

Method Summary

Methods inherited from interface java.util.Comparator

Methods inherited from class java.lang.Object

Constructor Detail

SAMRecordDuplicateComparator

SAMRecordDuplicateComparator

Method Detail

setScoringStrategy

compare

duplicateSetCompare

fileOrderCompare