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 String getSortKey​(SAMRecord rec)

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