SAMRecordQueryHashComparator (htsjdk 2.8.1 API)

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java.lang.Object
- htsjdk.samtools.SAMRecordQueryNameComparator
- - htsjdk.samtools.SAMRecordQueryHashComparator

All Implemented Interfaces:

SAMRecordComparator, Serializable, Comparator<SAMRecord>
```
public class SAMRecordQueryHashComparator
extends SAMRecordQueryNameComparator
implements Serializable
```
SAMRecord comparator that provides an ordering based on a hash of the queryname. Has the useful property that reads with the same name will be grouped together, but that reads appear in an otherwise random order. Useful for when the read names in a BAM are correlated to something else (e.g. position, read group), making a straight queryname sort undesirable.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

SAMRecordQueryHashComparator()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compare(SAMRecord lhs, SAMRecord rhs)` Compares two records based on an integer hash of their read name's.
`int`	`fileOrderCompare(SAMRecord lhs, SAMRecord rhs)` Compares two records based on an integer hash of their read names.

Methods inherited from class htsjdk.samtools.SAMRecordQueryNameComparator
compareReadNames

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

Methods inherited from interface java.util.Comparator
comparing, comparing, comparingDouble, comparingInt, comparingLong, equals, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

- Constructor Detail
  - SAMRecordQueryHashComparator
```
public SAMRecordQueryHashComparator()
```
- Method Detail
  - compare
```
public int compare(SAMRecord lhs,
                   SAMRecord rhs)
```
    Compares two records based on an integer hash of their read name's. If the hash values are equal, falls back to the behaviour of SAMRecordQueryNameComparator to break the tie.
    
    Specified by:
    
    compare in interface Comparator<SAMRecord>
    
    Overrides:
    
    compare in class SAMRecordQueryNameComparator
  - fileOrderCompare
```
public int fileOrderCompare(SAMRecord lhs,
                            SAMRecord rhs)
```
    Compares two records based on an integer hash of their read names. If the hash values are equal, falls back to the behaviour of SAMRecordQueryNameComparator to break the tie.
    
    Specified by:
    
    fileOrderCompare in interface SAMRecordComparator
    
    Overrides:
    
    fileOrderCompare in class SAMRecordQueryNameComparator
    
    Returns:
    
    negative if samRecord1 < samRecord2, 0 if equal, else positive

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