SAMSortOrderChecker (htsjdk 2.23.0 API)

java.lang.Object
- htsjdk.samtools.SAMSortOrderChecker

public class SAMSortOrderChecker
extends Object

Encapsulates simple check for SAMRecord order.

Constructor Summary

Constructors
Constructor Description

SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`SAMRecord`	`getPreviousRecord()`
`String`	`getSortKey(SAMRecord rec)`	Return the sort key used for the given sort order.
`SAMFileHeader.SortOrder`	`getSortOrder()`
`boolean`	`isSorted(SAMRecord rec)`	Check if given SAMRecord violates sort order relative to previous SAMRecord.

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

- Constructor Detail
  - SAMSortOrderChecker
```
public SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)
```
- Method Detail
  - isSorted
```
public boolean isSorted(SAMRecord rec)
```
    Check if given SAMRecord violates sort order relative to previous SAMRecord.
    
    Returns:
    
    True if sort order is unsorted, if this is the first record, or if previous <= rec.
  - getPreviousRecord
```
public SAMRecord getPreviousRecord()
```
  - getSortOrder
```
public SAMFileHeader.SortOrder getSortOrder()
```
  - getSortKey
```
public String getSortKey(SAMRecord rec)
```
    Return the sort key used for the given sort order. Useful in error messages. This should only be used in error messages and program correctness should not rely on this.