htsjdk.samtools

Class SAMSequenceDictionary

java.lang.Object

htsjdk.samtools.SAMSequenceDictionary

All Implemented Interfaces:

HtsHeader, java.io.Serializable

public class SAMSequenceDictionary
extends java.lang.Object
implements HtsHeader, java.io.Serializable

Collection of SAMSequenceRecords.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.List<java.lang.String>	DEFAULT_DICTIONARY_EQUAL_TAG
static long	serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMSequenceDictionary()
SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list)

Method Summary

Modifier and Type	Method and Description
SAMSequenceRecord	addAlternativeSequenceName(java.lang.String originalName, java.lang.String altName) Add an alternative sequence name (AN tag) to a SAMSequenceRecord, including it into the aliases to retrieve the contigs (as with addSequenceAlias(String, String).
void	addSequence(SAMSequenceRecord sequenceRecord)
SAMSequenceRecord	addSequenceAlias(java.lang.String originalName, java.lang.String altName) Add an alias to a SAMSequenceRecord.
void	assertSameDictionary(SAMSequenceDictionary that) Non-comprehensive equals(Object)-assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).
boolean	equals(java.lang.Object o) Returns true if the two dictionaries are the same.
long	getReferenceLength()
SAMSequenceRecord	getSequence(int sequenceIndex)
SAMSequenceRecord	getSequence(java.lang.String name)
int	getSequenceIndex(java.lang.String sequenceName)
java.util.List<SAMSequenceRecord>	getSequences()
int	hashCode()
boolean	isEmpty()
boolean	isSameDictionary(SAMSequenceDictionary that) Non-comprehensive equals(Object)-validation: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).
java.lang.String	md5() return a MD5 sum for ths dictionary, the checksum is re-computed each time this method is called.
static SAMSequenceDictionary	mergeDictionaries(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2, java.util.List<java.lang.String> tagsToMatch) Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences.
void	setSequences(java.util.List<SAMSequenceRecord> list) Replaces the existing list of SAMSequenceRecords with the given list.
int	size()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

DEFAULT_DICTIONARY_EQUAL_TAG

public static final java.util.List<java.lang.String> DEFAULT_DICTIONARY_EQUAL_TAG

Constructor Detail

SAMSequenceDictionary

public SAMSequenceDictionary()

SAMSequenceDictionary

public SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list)

Method Detail

getSequences

public java.util.List<SAMSequenceRecord> getSequences()

getSequence

public SAMSequenceRecord getSequence(java.lang.String name)

setSequences

public void setSequences(java.util.List<SAMSequenceRecord> list)

Replaces the existing list of SAMSequenceRecords with the given list. Reset the aliases

Parameters:

list - This value is copied and validated.

addSequence

public void addSequence(SAMSequenceRecord sequenceRecord)

getSequence

public SAMSequenceRecord getSequence(int sequenceIndex)

Returns:

The SAMSequenceRecord with the given index, or null if index is out of range.

getSequenceIndex

public int getSequenceIndex(java.lang.String sequenceName)

Returns:

The index for the given sequence name, or if the name is not found.

size

public int size()

Returns:

number of SAMSequenceRecord(s) in this dictionary

getReferenceLength

public long getReferenceLength()

Returns:

The sum of the lengths of the sequences in this dictionary

isEmpty

public boolean isEmpty()

Returns:

true is the dictionary is empty

assertSameDictionary

public void assertSameDictionary(SAMSequenceDictionary that)

Non-comprehensive equals(Object)-assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord). Aliases are ignored.

Throws:

java.lang.AssertionError - When the dictionaries are not the same, with some human-readable information as to why

isSameDictionary

public boolean isSameDictionary(SAMSequenceDictionary that)

Non-comprehensive equals(Object)-validation: instead of calling SAMSequenceRecord.equals(Object) on constituent SAMSequenceRecords in this dictionary against its pair in the target dictionary, in order, call SAMSequenceRecord.isSameSequence(SAMSequenceRecord).

Parameters:

that - SAMSequenceDictionary to compare against

Returns:

true if the dictionaries are the same, false otherwise

equals

public boolean equals(java.lang.Object o)

Returns true if the two dictionaries are the same.

NOTE: Aliases are NOT considered, but alternative sequence names (AN tag) names ARE.

Overrides:

equals in class java.lang.Object

addSequenceAlias

public SAMSequenceRecord addSequenceAlias(java.lang.String originalName,
                                          java.lang.String altName)

Add an alias to a SAMSequenceRecord. This can be use to provide some alternate names fo a given contig. e.g: 1,chr1,chr01,01,CM000663,NC_000001.10 e.g: MT,chrM

NOTE: this method does not add the alias to the alternative sequence name tag (AN) in the SAMSequenceRecord. If you would like to add it to the AN tag, use addAlternativeSequenceName(String, String) instead.

Parameters:

originalName - existing contig name

altName - new contig name

Returns:

the contig associated to the 'originalName/altName'

addAlternativeSequenceName

public SAMSequenceRecord addAlternativeSequenceName(java.lang.String originalName,
                                                    java.lang.String altName)

Add an alternative sequence name (AN tag) to a SAMSequenceRecord, including it into the aliases to retrieve the contigs (as with addSequenceAlias(String, String).

This can be use to provide some alternate names fo a given contig. e.g: 1,chr1,chr01,01,CM000663 or MT,chrM.

Parameters:

originalName - existing contig name

altName - new contig name

Returns:

the contig associated to the 'originalName/altName', with the AN tag including the altName

md5

public java.lang.String md5()

return a MD5 sum for ths dictionary, the checksum is re-computed each time this method is called.

 md5( (seq1.md5_if_available) + ' '+(seq2.name+seq2.length) + ' '+...)
 

Returns:

a MD5 checksum for this dictionary or the empty string if it is empty

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

mergeDictionaries

public static SAMSequenceDictionary mergeDictionaries(SAMSequenceDictionary dict1,
                                                      SAMSequenceDictionary dict2,
                                                      java.util.List<java.lang.String> tagsToMatch)

Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences. Requires that dictionaries have the same SAMSequence records in the same order. For each sequenceIndex, the union of the tags from both sequences will be added to the new sequence, mismatching values (for tags that are in both) will generate a warning, and the value from dict1 will be used. For tags that are in tagsToEquate an unequal value will generate an error (an IllegalArgumentException will be thrown.) tagsToEquate must include LN and MD.

Parameters:

dict1 - first dictionary

dict2 - first dictionary

tagsToMatch - list of tags that must be equal if present in both sequence. Must contain MD, and LN

Returns:

dictionary consisting of the same sequences as the two inputs with the merged values of tags.