public class SAMFileHeader extends AbstractSAMHeaderRecord
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.
|
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 |
serialVersionUID
Constructor and Description |
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SAMFileHeader() |
SAMFileHeader(SAMSequenceDictionary dict)
Constructor that initializes the sequence dictionary with the provided one.
|
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() |
java.lang.String |
getSAMString()
Returns the record in the SAM line-based text format.
|
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 |
setAttribute(java.lang.String key,
java.lang.Object value)
Deprecated.
Use {@link #setAttribute(String, String) instead
|
void |
setAttribute(java.lang.String key,
java.lang.String value)
Set the given value for the attribute named 'key'.
|
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.
|
attributesEqual, attributesHashCode, getAttribute, getAttributes, getId, toString
public static final java.lang.String VERSION_TAG
public static final java.lang.String SORT_ORDER_TAG
public static final java.lang.String GROUP_ORDER_TAG
public static final java.lang.String CURRENT_VERSION
public static final java.util.Set<java.lang.String> ACCEPTABLE_VERSIONS
public static final java.util.Set<java.lang.String> STANDARD_TAGS
public SAMFileHeader()
public SAMFileHeader(SAMSequenceDictionary dict)
public java.lang.String getVersion()
public java.lang.String getCreator()
public SAMSequenceDictionary getSequenceDictionary()
public java.util.List<SAMReadGroupRecord> getReadGroups()
public SAMSequenceRecord getSequence(java.lang.String name)
public SAMReadGroupRecord getReadGroup(java.lang.String name)
public void setSequenceDictionary(SAMSequenceDictionary sequenceDictionary)
public void addSequence(SAMSequenceRecord sequenceRecord)
public SAMSequenceRecord getSequence(int sequenceIndex)
public int getSequenceIndex(java.lang.String sequenceName)
public void setReadGroups(java.util.List<SAMReadGroupRecord> readGroups)
public void addReadGroup(SAMReadGroupRecord readGroup)
public java.util.List<SAMProgramRecord> getProgramRecords()
public void addProgramRecord(SAMProgramRecord programRecord)
public SAMProgramRecord getProgramRecord(java.lang.String pgId)
public void setProgramRecords(java.util.List<SAMProgramRecord> programRecords)
programRecords
- This list is used directly, not copied.public SAMProgramRecord createProgramRecord()
public SAMFileHeader.SortOrder getSortOrder()
public void setSortOrder(SAMFileHeader.SortOrder so)
public SAMFileHeader.GroupOrder getGroupOrder()
public void setGroupOrder(SAMFileHeader.GroupOrder go)
@Deprecated public void setAttribute(java.lang.String key, java.lang.Object value)
setAttribute
in class AbstractSAMHeaderRecord
key
- attribute namevalue
- attribute valuepublic void setAttribute(java.lang.String key, java.lang.String value)
setAttribute
in class AbstractSAMHeaderRecord
key
- attribute namevalue
- attribute valuepublic java.lang.String getTextHeader()
public void setTextHeader(java.lang.String textHeader)
public java.util.List<java.lang.String> getComments()
public void addComment(java.lang.String comment)
public void setComments(java.util.Collection<java.lang.String> comments)
public java.util.List<SAMValidationError> getValidationErrors()
public void addValidationError(SAMValidationError error)
public void setValidationErrors(java.util.Collection<SAMValidationError> errors)
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public final SAMFileHeader clone()
clone
in class java.lang.Object
public java.lang.String getSAMString()
AbstractSAMHeaderRecord
getSAMString
in class AbstractSAMHeaderRecord