Field Detail

• VERSION_TAG

  public static final String VERSION_TAG

  See Also:

  Constant Field Values

• SORT_ORDER_TAG

  public static final String SORT_ORDER_TAG

  See Also:

  Constant Field Values

• GROUP_ORDER_TAG

  public static final String GROUP_ORDER_TAG

  See Also:

  Constant Field Values

• CURRENT_VERSION

  public static final String CURRENT_VERSION

  See Also:

  Constant Field Values

• ACCEPTABLE_VERSIONS

  public static final Set<String> ACCEPTABLE_VERSIONS

• STANDARD_TAGS

  public static final Set<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 String getVersion()

• getCreator

  public String getCreator()

• getSequenceDictionary

  public SAMSequenceDictionary getSequenceDictionary()

• getReadGroups

  public List<SAMReadGroupRecord> getReadGroups()

• getSequence

  public SAMSequenceRecord getSequence​(String name)

  Look up sequence record by name.

  Returns:

  sequence record if it's found by name, or null if sequence dictionary is empty or if the sequence is not found in the dictionary.

• getReadGroup

  public SAMReadGroupRecord getReadGroup​(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​(String sequenceName)

  Returns:

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

• setReadGroups

  public void setReadGroups​(List<SAMReadGroupRecord> readGroups)

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

• addReadGroup

  public void addReadGroup​(SAMReadGroupRecord readGroup)

• getProgramRecords

  public List<SAMProgramRecord> getProgramRecords()

• addProgramRecord

  public void addProgramRecord​(SAMProgramRecord programRecord)

• getProgramRecord

  public SAMProgramRecord getProgramRecord​(String pgId)

• setProgramRecords

  public void setProgramRecords​(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)

• setAttribute

  @Deprecated
  public void setAttribute​(String key,
                           Object value)

  Deprecated.

  Use instead
  Set the given value for the attribute named 'key'. Replaces an existing value, if any. If value is null, the attribute is removed. Otherwise, the value will be converted to a String with toString.

  Overrides:

  setAttribute in class AbstractSAMHeaderRecord

  Parameters:

  key - attribute name

  value - attribute value

• setAttribute

  public void setAttribute​(String key,
                           String value)

  Set the given value for the attribute named 'key'. Replaces an existing value, if any. If value is null, the attribute is removed.

  Overrides:

  setAttribute in class AbstractSAMHeaderRecord

  Parameters:

  key - attribute name

  value - attribute value

• getTextHeader

  public 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​(String textHeader)

• getComments

  public List<String> getComments()

• addComment

  public void addComment​(String comment)

• setComments

  public void setComments​(Collection<String> comments)

  Replace existing comments with the contents of the given collection.

• getValidationErrors

  public List<SAMValidationError> getValidationErrors()

• addValidationError

  public void addValidationError​(SAMValidationError error)

• setValidationErrors

  public void setValidationErrors​(Collection<SAMValidationError> errors)

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

• equals

  public boolean equals​(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object

• clone

  public final SAMFileHeader clone()

  Overrides:

  clone in class Object

• getSAMString

  public String getSAMString()

  Description copied from class: AbstractSAMHeaderRecord
  Returns the record in the SAM line-based text format. Fields are separated by '\t' characters. The String is NOT terminated by '\n'.

  Specified by:

  getSAMString in class AbstractSAMHeaderRecord