SAMRecordQueryNameComparator (htsjdk 2.14.3 API)

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java.lang.Object
- htsjdk.samtools.SAMRecordQueryNameComparator

All Implemented Interfaces:

SAMRecordComparator, Serializable, Comparator<SAMRecord>

Direct Known Subclasses:

SAMRecordQueryHashComparator
```
public class SAMRecordQueryNameComparator
extends Object
implements SAMRecordComparator, Serializable
```
Comparator for "queryname" ordering of SAMRecords.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

SAMRecordQueryNameComparator()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`compare(SAMRecord samRecord1, SAMRecord samRecord2)`
`static int`	`compareReadNames(String readName1, String readName2)`	Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.
`int`	`fileOrderCompare(SAMRecord samRecord1, SAMRecord samRecord2)`	Less stringent compare method than the regular compare.

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
  - SAMRecordQueryNameComparator
```
public SAMRecordQueryNameComparator()
```
- Method Detail
  - compare
```
public int compare(SAMRecord samRecord1,
                   SAMRecord samRecord2)
```
    Specified by:
    
    compare in interface Comparator<SAMRecord>
  - fileOrderCompare
```
public int fileOrderCompare(SAMRecord samRecord1,
                            SAMRecord samRecord2)
```
    Less stringent compare method than the regular compare. If the two records are equal enough that their ordering in a sorted SAM file would be arbitrary, this method returns 0.
    
    Specified by:
    
    fileOrderCompare in interface SAMRecordComparator
    
    Returns:
    
    negative if samRecord1 < samRecord2, 0 if equal, else positive
  - compareReadNames
```
public static int compareReadNames(String readName1,
                                   String readName2)
```
    Encapsulate algorithm for comparing read names in queryname-sorted file, since there have been conversations about changing the behavior.

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