Package htsjdk.samtools

Class SAMSortOrderChecker

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

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 Details

SAMSortOrderChecker

public SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)

Method Details

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.