htsjdk.samtools

Class SAMFileHeader

java.lang.Object

htsjdk.samtools.AbstractSAMHeaderRecord

htsjdk.samtools.SAMFileHeader

All Implemented Interfaces:

java.io.Serializable

public class SAMFileHeader
extends AbstractSAMHeaderRecord

Header information from a SAM or BAM file.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SAMFileHeader.GroupOrder
static class	SAMFileHeader.PgIdGenerator Little class to generate program group IDs
static class	SAMFileHeader.SortOrder Ways in which a SAM or BAM may be sorted.

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Set<java.lang.String>	ACCEPTABLE_VERSIONS
static java.lang.String	CURRENT_VERSION
static java.lang.String	GROUP_ORDER_TAG
static java.lang.String	SORT_ORDER_TAG
static java.util.Set<java.lang.String>	STANDARD_TAGS These tags are of known type, so don't need a type field in the text representation.
static java.lang.String	VERSION_TAG

Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

serialVersionUID

Constructor Summary

Constructors

Constructor and Description
SAMFileHeader()
SAMFileHeader(SAMSequenceDictionary dict) Constructor that initializes the sequence dictionary with the provided one.

Method Summary

Modifier and Type	Method and Description
void	addComment(java.lang.String comment)
void	addProgramRecord(SAMProgramRecord programRecord)
void	addReadGroup(SAMReadGroupRecord readGroup)
void	addSequence(SAMSequenceRecord sequenceRecord)
void	addValidationError(SAMValidationError error)
SAMFileHeader	clone()
SAMProgramRecord	createProgramRecord()
boolean	equals(java.lang.Object o)
java.util.List<java.lang.String>	getComments()
java.lang.String	getCreator()
SAMFileHeader.GroupOrder	getGroupOrder()
SAMProgramRecord	getProgramRecord(java.lang.String pgId)
java.util.List<SAMProgramRecord>	getProgramRecords()
SAMReadGroupRecord	getReadGroup(java.lang.String name) Look up read group record by name.
java.util.List<SAMReadGroupRecord>	getReadGroups()
SAMSequenceRecord	getSequence(int sequenceIndex) Look up a sequence record by index.
SAMSequenceRecord	getSequence(java.lang.String name) Look up sequence record by name.
SAMSequenceDictionary	getSequenceDictionary()
int	getSequenceIndex(java.lang.String sequenceName)
SAMFileHeader.SortOrder	getSortOrder()
java.lang.String	getTextHeader() If this SAMHeader was read from a file, this property contains the header as it appeared in the file, otherwise it is null.
java.util.List<SAMValidationError>	getValidationErrors()
java.lang.String	getVersion()
int	hashCode()
void	setComments(java.util.Collection<java.lang.String> comments) Replace existing comments with the contents of the given collection.
void	setGroupOrder(SAMFileHeader.GroupOrder go)
void	setProgramRecords(java.util.List<SAMProgramRecord> programRecords) Replace entire list of program records
void	setReadGroups(java.util.List<SAMReadGroupRecord> readGroups) Replace entire list of read groups.
void	setSequenceDictionary(SAMSequenceDictionary sequenceDictionary) Replace entire sequence dictionary.
void	setSortOrder(SAMFileHeader.SortOrder so)
void	setTextHeader(java.lang.String textHeader)
void	setValidationErrors(java.util.Collection<SAMValidationError> errors) Replace list of validation errors with the elements of the given list.

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

attributesEqual, attributesHashCode, getAttribute, getAttributes, getId, setAttribute, setAttribute, toString

Methods inherited from class java.lang.Object

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

Field Detail

VERSION_TAG

public static final java.lang.String VERSION_TAG

See Also:

Constant Field Values

SORT_ORDER_TAG

public static final java.lang.String SORT_ORDER_TAG

See Also:

Constant Field Values

GROUP_ORDER_TAG

public static final java.lang.String GROUP_ORDER_TAG

See Also:

Constant Field Values

CURRENT_VERSION

public static final java.lang.String CURRENT_VERSION

See Also:

Constant Field Values

ACCEPTABLE_VERSIONS

public static final java.util.Set<java.lang.String> ACCEPTABLE_VERSIONS

STANDARD_TAGS

public static final java.util.Set<java.lang.String> STANDARD_TAGS

These tags are of known type, so don't need a type field in the text representation.

Constructor Detail

SAMFileHeader

public SAMFileHeader()

SAMFileHeader

public SAMFileHeader(SAMSequenceDictionary dict)

Constructor that initializes the sequence dictionary with the provided one.

Method Detail

getVersion

public java.lang.String getVersion()

getCreator

public java.lang.String getCreator()

getSequenceDictionary

public SAMSequenceDictionary getSequenceDictionary()

getReadGroups

public java.util.List<SAMReadGroupRecord> getReadGroups()

getSequence

public SAMSequenceRecord getSequence(java.lang.String name)

Look up sequence record by name.

getReadGroup

public SAMReadGroupRecord getReadGroup(java.lang.String name)

Look up read group record by name.

setSequenceDictionary

public void setSequenceDictionary(SAMSequenceDictionary sequenceDictionary)

Replace entire sequence dictionary. The given sequence dictionary is stored, not copied.

addSequence

public void addSequence(SAMSequenceRecord sequenceRecord)

getSequence

public SAMSequenceRecord getSequence(int sequenceIndex)

Look up a sequence record by index. First sequence in the header is the 0th.

Returns:

The corresponding sequence record, or null if the index is out of range.

getSequenceIndex

public int getSequenceIndex(java.lang.String sequenceName)

Returns:

Sequence index for the given sequence name, or -1 if the name is not found.

setReadGroups

public void setReadGroups(java.util.List<SAMReadGroupRecord> readGroups)

Replace entire list of read groups. The given list is stored, not copied.

addReadGroup

public void addReadGroup(SAMReadGroupRecord readGroup)

getProgramRecords

public java.util.List<SAMProgramRecord> getProgramRecords()

addProgramRecord

public void addProgramRecord(SAMProgramRecord programRecord)

getProgramRecord

public SAMProgramRecord getProgramRecord(java.lang.String pgId)

setProgramRecords

public void setProgramRecords(java.util.List<SAMProgramRecord> programRecords)

Replace entire list of program records

Parameters:

programRecords - This list is used directly, not copied.

createProgramRecord

public SAMProgramRecord createProgramRecord()

Returns:

a new SAMProgramRecord with an ID guaranteed to not exist in this SAMFileHeader

getSortOrder

public SAMFileHeader.SortOrder getSortOrder()

setSortOrder

public void setSortOrder(SAMFileHeader.SortOrder so)

getGroupOrder

public SAMFileHeader.GroupOrder getGroupOrder()

setGroupOrder

public void setGroupOrder(SAMFileHeader.GroupOrder go)

getTextHeader

public java.lang.String getTextHeader()

If this SAMHeader was read from a file, this property contains the header as it appeared in the file, otherwise it is null. Note that this is not a toString() operation. Changes to the SAMFileHeader object after reading from the file are not reflected in this value. In addition this value is only set if one of the following is true: - The size of the header is < 1,048,576 characters (1MB ascii, 2MB unicode) - There are either validation or parsing errors associated with the header Invalid header lines may appear in value but are not stored in the SAMFileHeader object.

setTextHeader

public void setTextHeader(java.lang.String textHeader)

getComments

public java.util.List<java.lang.String> getComments()

addComment

public void addComment(java.lang.String comment)

setComments

public void setComments(java.util.Collection<java.lang.String> comments)

Replace existing comments with the contents of the given collection.

getValidationErrors

public java.util.List<SAMValidationError> getValidationErrors()

addValidationError

public void addValidationError(SAMValidationError error)

setValidationErrors

public void setValidationErrors(java.util.Collection<SAMValidationError> errors)

Replace list of validation errors with the elements of the given list.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

clone

public final SAMFileHeader clone()

Overrides:

clone in class java.lang.Object