Package htsjdk.samtools
Class SAMProgramRecord
- java.lang.Object
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- htsjdk.samtools.AbstractSAMHeaderRecord
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- htsjdk.samtools.SAMProgramRecord
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- All Implemented Interfaces:
Serializable
public class SAMProgramRecord extends AbstractSAMHeaderRecord
In-memory representation of @PG SAM header record.- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static String
COMMAND_LINE_TAG
static String
PREVIOUS_PROGRAM_GROUP_ID_TAG
static String
PROGRAM_GROUP_ID_TAG
static String
PROGRAM_NAME_TAG
static String
PROGRAM_VERSION_TAG
static Set<String>
STANDARD_TAGS
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Fields inherited from class htsjdk.samtools.AbstractSAMHeaderRecord
serialVersionUID
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Constructor Summary
Constructors Constructor Description SAMProgramRecord(String programGroupId)
SAMProgramRecord(String id, SAMProgramRecord srcProgramRecord)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Methods inherited from class htsjdk.samtools.AbstractSAMHeaderRecord
attributesEqual, attributesHashCode, getAttribute, getAttributes, setAttribute, setAttribute, toString
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Field Detail
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PROGRAM_GROUP_ID_TAG
public static final String PROGRAM_GROUP_ID_TAG
- See Also:
- Constant Field Values
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PROGRAM_NAME_TAG
public static final String PROGRAM_NAME_TAG
- See Also:
- Constant Field Values
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PROGRAM_VERSION_TAG
public static final String PROGRAM_VERSION_TAG
- See Also:
- Constant Field Values
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COMMAND_LINE_TAG
public static final String COMMAND_LINE_TAG
- See Also:
- Constant Field Values
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PREVIOUS_PROGRAM_GROUP_ID_TAG
public static final String PREVIOUS_PROGRAM_GROUP_ID_TAG
- See Also:
- Constant Field Values
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Constructor Detail
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SAMProgramRecord
public SAMProgramRecord(String programGroupId)
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SAMProgramRecord
public SAMProgramRecord(String id, SAMProgramRecord srcProgramRecord)
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Method Detail
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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 classAbstractSAMHeaderRecord
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getProgramGroupId
public String getProgramGroupId()
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getProgramName
public String getProgramName()
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setProgramName
public void setProgramName(String name)
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getProgramVersion
public String getProgramVersion()
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setProgramVersion
public void setProgramVersion(String version)
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getCommandLine
public String getCommandLine()
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setCommandLine
public void setCommandLine(String commandLine)
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getPreviousProgramGroupId
public String getPreviousProgramGroupId()
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setPreviousProgramGroupId
public void setPreviousProgramGroupId(String id)
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equivalent
public boolean equivalent(SAMProgramRecord that)
- Returns:
- true if this == that except for the program group ID, which is arbitrary
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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 classAbstractSAMHeaderRecord
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