Package htsjdk.samtools
Class SAMSortOrderChecker
- java.lang.Object
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- htsjdk.samtools.SAMSortOrderChecker
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public class SAMSortOrderChecker extends Object
Encapsulates simple check for SAMRecord order.
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Constructor Summary
Constructors Constructor Description SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)
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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.
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Constructor Detail
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SAMSortOrderChecker
public SAMSortOrderChecker(SAMFileHeader.SortOrder sortOrder)
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Method Detail
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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.
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getPreviousRecord
public SAMRecord getPreviousRecord()
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getSortOrder
public SAMFileHeader.SortOrder getSortOrder()
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