Package picard.util

Class SequenceDictionaryUtils

java.lang.Object
picard.util.SequenceDictionaryUtils
public class SequenceDictionaryUtils extends Object
Class with helper methods for generating and writing SequenceDictionary objects.

  • Constructor Details

    • SequenceDictionaryUtils

      public SequenceDictionaryUtils()

  • Method Details

    • encodeDictionary

      public static void encodeDictionary(BufferedWriter writer, Iterator<htsjdk.samtools.SAMSequenceRecord> samSequenceRecordIterator)
      Encodes a sequence dictionary
      Parameters:
      writer - a Buffered writer into which the dictionary will be written
      samSequenceRecordIterator - an iterator that produces SAMSequenceRecords
      Throws:
      IllegalArgumentException - if the iterator produces two SAMSequenceRecord with the same name

    • makeSortingCollection

      public static htsjdk.samtools.util.SortingCollection<String> makeSortingCollection()

    • assertSequenceDictionariesEqual

      public static void assertSequenceDictionariesEqual(htsjdk.samtools.SAMSequenceDictionary firstDict, String firstDictSource, htsjdk.samtools.SAMSequenceDictionary secondDict, String secondDictSource)
      Throw an exception if the two provided sequence dictionaries are not equal.
      Parameters:
      firstDict - first dictionary to compare
      firstDictSource - a user-recognizable message identifying the source of the first dictionary, preferably a file path
      secondDict - second dictionary to compare
      secondDictSource - a user-recognizable message identifying the source of the second dictionary, preferably a file path