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.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SequenceDictionaryUtils.SamSequenceRecordsIterator

Constructor Summary

Constructors

Constructor	Description
SequenceDictionaryUtils()

Method Summary

Modifier and Type	Method	Description
static void	encodeDictionary(BufferedWriter writer, Iterator<htsjdk.samtools.SAMSequenceRecord> samSequenceRecordIterator)	Encodes a sequence dictionary
static htsjdk.samtools.util.SortingCollection<String>	makeSortingCollection()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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()