htsjdk.samtools

Class SAMSortOrderChecker

java.lang.Object

htsjdk.samtools.SAMSortOrderChecker

public class SAMSortOrderChecker
extends java.lang.Object

Encapsulates simple check for SAMRecord order.

Constructor Summary

Constructors

Constructor and Description
SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)

Method Summary

Methods

Modifier and Type	Method and Description
SAMRecord	getPreviousRecord()
java.lang.String	getSortKey(SAMRecord rec) Return the sort key used for the given sort order.
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()

getSortKey

public java.lang.String getSortKey(SAMRecord rec)

Return the sort key used for the given sort order. Useful in error messages.