Package htsjdk.samtools

Class SAMProgramRecord

java.lang.Object

htsjdk.samtools.AbstractSAMHeaderRecord

htsjdk.samtools.SAMProgramRecord

All Implemented Interfaces:

Serializable

public class SAMProgramRecord
extends AbstractSAMHeaderRecord

In-memory representation of @PG SAM header record.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMMAND_LINE_TAG
static final String	PREVIOUS_PROGRAM_GROUP_ID_TAG
static final String	PROGRAM_GROUP_ID_TAG
static final String	PROGRAM_NAME_TAG
static final String	PROGRAM_VERSION_TAG
static final Set<String>	STANDARD_TAGS

Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

serialVersionUID

Constructor Summary

Constructors

Constructor	Description
SAMProgramRecord(String programGroupId)
SAMProgramRecord(String id, SAMProgramRecord srcProgramRecord)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
boolean	equivalent(SAMProgramRecord that)
String	getCommandLine()
String	getId()	Returns the ID tag (or equivalent) for this header record.
String	getPreviousProgramGroupId()
String	getProgramGroupId()
String	getProgramName()
String	getProgramVersion()
String	getSAMString()	Returns the record in the SAM line-based text format.
int	hashCode()
void	setCommandLine(String commandLine)
void	setPreviousProgramGroupId(String id)
void	setProgramName(String name)
void	setProgramVersion(String version)

Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord

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

Methods inherited from class java.lang.Object

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

Field Details

PROGRAM_GROUP_ID_TAG

public static final String PROGRAM_GROUP_ID_TAG

See Also:

• Constant Field Values

PROGRAM_NAME_TAG

public static final String PROGRAM_NAME_TAG

See Also:

• Constant Field Values

PROGRAM_VERSION_TAG

public static final String PROGRAM_VERSION_TAG

See Also:

• Constant Field Values

COMMAND_LINE_TAG

public static final String COMMAND_LINE_TAG

See Also:

• Constant Field Values

PREVIOUS_PROGRAM_GROUP_ID_TAG

public static final String PREVIOUS_PROGRAM_GROUP_ID_TAG

See Also:

• Constant Field Values

STANDARD_TAGS

public static final Set<String> STANDARD_TAGS

Constructor Details

SAMProgramRecord

public SAMProgramRecord(String programGroupId)

SAMProgramRecord

public SAMProgramRecord(String id,
 SAMProgramRecord srcProgramRecord)

Method Details

getId

public String getId()

Description copied from class: AbstractSAMHeaderRecord

Returns the ID tag (or equivalent) for this header record. The default implementation throws a SAMException to indicate "not implemented".

Overrides:

getId in class AbstractSAMHeaderRecord

getProgramGroupId

public String getProgramGroupId()

getProgramName

public String getProgramName()

setProgramName

public void setProgramName(String name)

getProgramVersion

public String getProgramVersion()

setProgramVersion

public void setProgramVersion(String version)

getCommandLine

public String getCommandLine()

setCommandLine

public void setCommandLine(String commandLine)

getPreviousProgramGroupId

public String getPreviousProgramGroupId()

setPreviousProgramGroupId

public void setPreviousProgramGroupId(String id)

equivalent

public boolean equivalent(SAMProgramRecord that)

Returns:

true if this == that except for the program group ID, which is arbitrary

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode 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