java.lang.Object
- picard.cmdline.StandardOptionDefinitions

```
public class StandardOptionDefinitions
extends Object
```
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`ASSUME_SORT_ORDER_SHORT_NAME`
`static String`	`ASSUME_SORTED_SHORT_NAME`
`static String`	`EXPECTED_INSERT_SIZE_SHORT_NAME`
`static String`	`INPUT_SHORT_NAME`
`static String`	`LANE_SHORT_NAME`
`static String`	`LIBRARY_NAME_SHORT_NAME`
`static String`	`METRICS_FILE_SHORT_NAME`
`static String`	`MINIMUM_LOD_SHORT_NAME`
`static String`	`MINIMUM_MAPPING_QUALITY_SHORT_NAME`
`static String`	`OUTPUT_SHORT_NAME`
`static String`	`PF_READS_ONLY_SHORT_NAME`
`static String`	`PROGRAM_RECORD_ID_SHORT_NAME`
`static String`	`READ_GROUP_ID_SHORT_NAME`
`static String`	`REFERENCE_SHORT_NAME`
`static String`	`SAMPLE_ALIAS_SHORT_NAME`
`static String`	`SEQUENCE_DICTIONARY_SHORT_NAME`
`static String`	`SORT_ORDER_SHORT_NAME`
`static String`	`USE_ORIGINAL_QUALITIES_SHORT_NAME`

Constructor Summary

Constructors
Constructor Description

StandardOptionDefinitions()

Method Summary
- Methods inherited from class java.lang.Object
  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - INPUT_SHORT_NAME
```
public static final String INPUT_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - OUTPUT_SHORT_NAME
```
public static final String OUTPUT_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - REFERENCE_SHORT_NAME
```
public static final String REFERENCE_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - SAMPLE_ALIAS_SHORT_NAME
```
public static final String SAMPLE_ALIAS_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - LIBRARY_NAME_SHORT_NAME
```
public static final String LIBRARY_NAME_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - EXPECTED_INSERT_SIZE_SHORT_NAME
```
public static final String EXPECTED_INSERT_SIZE_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - LANE_SHORT_NAME
```
public static final String LANE_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_DICTIONARY_SHORT_NAME
```
public static final String SEQUENCE_DICTIONARY_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - METRICS_FILE_SHORT_NAME
```
public static final String METRICS_FILE_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - ASSUME_SORTED_SHORT_NAME
```
public static final String ASSUME_SORTED_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - ASSUME_SORT_ORDER_SHORT_NAME
```
public static final String ASSUME_SORT_ORDER_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - PF_READS_ONLY_SHORT_NAME
```
public static final String PF_READS_ONLY_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - MINIMUM_MAPPING_QUALITY_SHORT_NAME
```
public static final String MINIMUM_MAPPING_QUALITY_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - READ_GROUP_ID_SHORT_NAME
```
public static final String READ_GROUP_ID_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - PROGRAM_RECORD_ID_SHORT_NAME
```
public static final String PROGRAM_RECORD_ID_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - MINIMUM_LOD_SHORT_NAME
```
public static final String MINIMUM_LOD_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - SORT_ORDER_SHORT_NAME
```
public static final String SORT_ORDER_SHORT_NAME
```
    See Also:
    
    Constant Field Values
  - USE_ORIGINAL_QUALITIES_SHORT_NAME
```
public static final String USE_ORIGINAL_QUALITIES_SHORT_NAME
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - StandardOptionDefinitions
```
public StandardOptionDefinitions()
```

Class StandardOptionDefinitions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

INPUT_SHORT_NAME

OUTPUT_SHORT_NAME

REFERENCE_SHORT_NAME

SAMPLE_ALIAS_SHORT_NAME

LIBRARY_NAME_SHORT_NAME

EXPECTED_INSERT_SIZE_SHORT_NAME

LANE_SHORT_NAME

SEQUENCE_DICTIONARY_SHORT_NAME

METRICS_FILE_SHORT_NAME

ASSUME_SORTED_SHORT_NAME

ASSUME_SORT_ORDER_SHORT_NAME

PF_READS_ONLY_SHORT_NAME

MINIMUM_MAPPING_QUALITY_SHORT_NAME

READ_GROUP_ID_SHORT_NAME

PROGRAM_RECORD_ID_SHORT_NAME

MINIMUM_LOD_SHORT_NAME

SORT_ORDER_SHORT_NAME

USE_ORIGINAL_QUALITIES_SHORT_NAME

Constructor Detail

StandardOptionDefinitions