LiftOverIntervalList (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.util.LiftOverIntervalList

```
@DocumentedFeature
public class LiftOverIntervalList
extends CommandLineProgram
```
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references. It is based on the UCSC LiftOver tool and uses a UCSC chain file to guide its operation. It accepts both Picard interval_list files or VCF files as interval inputs.

Usage example:
```
 java -jar picard.jar LiftOverIntervalList \
       I=input.interval_list \
       O=output.interval_list \
       SD=reference_sequence.dict \
       CHAIN=build.chain
 
```
Return codes
If all the intervals lifted over successfully, program will return 0. It will return 1 otherwise.

Caveats
An interval is "lifted" in its entirety, but it might intersect (a "hit") with multiple chain-blocks. Instead of placing the interval in multiple hits, it is lifted over using the first hit that passes the threshold of MIN_LIFTOVER_PCT. For large enough MIN_LIFTOVER_PCT this is non-ambiguous, but if one uses small values of MIN_LIFTOVER_PCT (perhaps in order to increase the rate of successful hits...) the liftover could end up going to the smaller of two good hits. On the other hand, if none of the hits pass the threshold a warning will be emitted and the interval will not be lifted.

- Field Summary
  
  Fields
  Modifier and Type Field Description
  
  File CHAIN
  
  File INPUT
  
  double MIN_LIFTOVER_PCT
  
  File OUTPUT
  
  File REJECT
  
  File SEQUENCE_DICTIONARY
  - Fields inherited from class picard.cmdline.CommandLineProgram
    COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
- Constructor Summary
  
  Constructors
  Constructor Description
  
  LiftOverIntervalList()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  protected int doWork()
  Do the work after command line has been parsed.
  - Methods inherited from class picard.cmdline.CommandLineProgram
    customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Fields
Modifier and Type	Field	Description
`File`	`CHAIN`
`File`	`INPUT`
`double`	`MIN_LIFTOVER_PCT`
`File`	`OUTPUT`
`File`	`REJECT`
`File`	`SEQUENCE_DICTIONARY`

Constructors
Constructor	Description
`LiftOverIntervalList()`

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.

Field Detail

INPUT

@Argument(doc="The input interval list to be lifted over.",
          shortName="I")
public File INPUT

OUTPUT

@Argument(doc="The output interval list file.",
          shortName="O")
public File OUTPUT

SEQUENCE_DICTIONARY

@Argument(doc="Sequence dictionary to place in the output interval list. (This should be the dictionary of the target reference.)",
          shortName="SD")
public File SEQUENCE_DICTIONARY

CHAIN

@Argument(doc="Chain file that guides the LiftOver process.")
public File CHAIN

MIN_LIFTOVER_PCT

@Argument(doc="Minimum percentage of bases in each input interval that must map to output interval for liftover of that interval to occur. If the program fails to find a good target for an interval, a warning will be emitted and the interval will be dropped from the output. ")
public double MIN_LIFTOVER_PCT

REJECT

@Argument(doc="Interval List file for intervals that were rejected",
          optional=true)
public File REJECT

Constructor Detail
- LiftOverIntervalList
```
public LiftOverIntervalList()
```

Method Detail
- doWork
```
protected int doWork()
```
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
  
  Specified by:
  
  doWork in class CommandLineProgram
  
  Returns:
  
  program exit status.

Class LiftOverIntervalList

Usage example:

Return codes

Caveats

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

SEQUENCE_DICTIONARY

CHAIN

MIN_LIFTOVER_PCT

REJECT

Constructor Detail

LiftOverIntervalList

Method Detail

doWork