picard.util

Class IntervalListTools

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.IntervalListTools

@DocumentedFeature
public class IntervalListTools
extends CommandLineProgram

Performs various IntervalList manipulations.

Summary

This tool offers multiple interval list file manipulation capabilities, including: sorting, merging, subtracting, padding, and other set-theoretic operations. The default action is to merge and sort the intervals provided in the INPUTs. Other options, e.g. interval subtraction, are controlled by the arguments.
Both IntervalList and VCF files are accepted as input. IntervalList should be denoted with the extension ".interval_list", while a VCF must have one of ".vcf", ".vcf.gz", ".bcf". When VCF file is used as input, each variant is translated into an using its reference allele or the END INFO annotation (if present) to determine the extent of the interval.

IntervalListTools can also "scatter" the resulting interval-list into many interval-files. This can be useful for creating multiple interval lists for scattering an analysis over.

Details

The IntervalList file format is designed to help the users avoid mixing references when supplying intervals and other genomic data to a single tool. A SAM style header must be present at the top of the file. After the header, the file then contains records, one per line in text format with the following values tab-separated:

 

 
Sequence name (SN)
 
Start position (1-based)
 
End position (1-based, end inclusive)
 
Strand (either + or -)
 
Interval name (ideally unique names for intervals)
 
 

The coordinate system is 1-based, closed-ended, so that the first base in a sequence is at position 1, and both the start and the end positions are included in an interval.

For Example:

 \@HD   VN:1.0
 \@SQ   SN:chr1 LN:501
 \@SQ   SN:chr2 LN:401
 chr1   1       100     +       starts at the first base of the contig and covers 100 bases
 chr2   100     100     +       interval with exactly one base
 

Usage examples

1. Combine the intervals from two interval lists:

 java -jar picard.jar IntervalListTools \\
       ACTION=CONCAT \\
       I=input.interval_list \\
       I=input_2.interval_list \\
       O=new.interval_list
 

2. Combine the intervals from two interval lists, sorting the resulting in list and merging overlapping and abutting intervals:

 java -jar picard.jar IntervalListTools \\
       ACTION=CONCAT \\
       SORT=true \\
       UNIQUE=true \\
       I=input.interval_list \\
       I=input_2.interval_list \\
       O=new.interval_list
 

3. Subtract the intervals in SECOND_INPUT from those in INPUT:

 java -jar picard.jar IntervalListTools \\
       ACTION=SUBTRACT \\
       I=input.interval_list \\
       SI=input_2.interval_list \\
       O=new.interval_list
 

4. Find bases that are in either input1.interval_list or input2.interval_list, and also in input3.interval_list:

 java -jar picard.jar IntervalListTools \\
       ACTION=INTERSECT \\
       I=input1.interval_list \\
       I=input2.interval_list \\
       SI=input3.interval_list \\
       O=new.interval_list
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IntervalListTools.Action

Field Summary

Fields

Modifier and Type	Field and Description
IntervalListTools.Action	ACTION
int	BREAK_BANDS_AT_MULTIPLES_OF
java.util.List<java.lang.String>	COMMENT
java.io.File	COUNT_OUTPUT
boolean	INCLUDE_FILTERED
java.util.List<java.io.File>	INPUT
boolean	INVERT
java.io.File	OUTPUT
picard.util.IntervalListTools.Output	OUTPUT_VALUE
int	PADDING
java.lang.Integer	SCATTER_CONTENT
int	SCATTER_COUNT
java.util.List<java.io.File>	SECOND_INPUT
boolean	SORT
IntervalListScatterMode	SUBDIVISION_MODE
boolean	UNIQUE

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
IntervalListTools()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getCommandLineParserForArgs, 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

Field Detail

INPUT

@Argument(shortName="I",
          doc="One or more interval lists. If multiple interval lists are provided the output is theresult of merging the inputs. Supported formats are interval_list and VCF.",
          minElements=1)
public java.util.List<java.io.File> INPUT

OUTPUT

@Argument(doc="The output interval list file to write (if SCATTER_COUNT == 1) or the directory into which to write the scattered interval sub-directories (if SCATTER_COUNT > 1).",
          shortName="O",
          optional=true)
public java.io.File OUTPUT

PADDING

@Argument(doc="The amount to pad each end of the intervals by before other operations are undertaken. Negative numbers are allowed and indicate intervals should be shrunk. Resulting intervals < 0 bases long will be removed. Padding is applied to the interval lists (both INPUT and SECOND_INPUT, if provided) <b> before </b> the ACTION is performed.",
          optional=true)
public int PADDING

UNIQUE

@Argument(doc="If true, merge overlapping and adjacent intervals to create a list of unique intervals. Implies SORT=true.")
public boolean UNIQUE

SORT

@Argument(doc="If true, sort the resulting interval list by coordinate.")
public boolean SORT

ACTION

@Argument(doc="Action to take on inputs.")
public IntervalListTools.Action ACTION

SECOND_INPUT

@Argument(shortName="SI",
          doc="Second set of intervals for SUBTRACT and DIFFERENCE operations.",
          optional=true)
public java.util.List<java.io.File> SECOND_INPUT

COMMENT

@Argument(doc="One or more lines of comment to add to the header of the output file (as @CO lines in the SAM header).",
          optional=true)
public java.util.List<java.lang.String> COMMENT

SCATTER_COUNT

@Argument(doc="The number of files into which to scatter the resulting list by locus; in some situations, fewer intervals may be emitted.  ")
public int SCATTER_COUNT

SCATTER_CONTENT

@Argument(doc="When scattering with this argument, each of the resultant files will (ideally) have this amount of \'content\', which  means either base-counts or interval-counts depending on SUBDIVISION_MODE. When provided, overrides SCATTER_COUNT",
          optional=true)
public java.lang.Integer SCATTER_CONTENT

INCLUDE_FILTERED

@Argument(doc="Whether to include filtered variants in the vcf when generating an interval list from vcf.",
          optional=true)
public boolean INCLUDE_FILTERED

BREAK_BANDS_AT_MULTIPLES_OF

@Argument(shortName="BRK",
          doc="If set to a positive value will create a new interval list with the original intervals broken up at integer multiples of this value. Set to 0 to NOT break up intervals.",
          optional=true)
public int BREAK_BANDS_AT_MULTIPLES_OF

SUBDIVISION_MODE

@Argument(shortName="M",
          doc="The mode used to scatter the interval list.")
public IntervalListScatterMode SUBDIVISION_MODE

INVERT

@Argument(doc="Produce the inverse list of intervals, that is, the regions in the genome that are <br>not</br> covered by any of the input intervals. Will merge abutting intervals first. Output will be sorted.",
          optional=true)
public boolean INVERT

OUTPUT_VALUE

@Argument(doc="What value to output to COUNT_OUTPUT file or stdout (for scripting).  If COUNT_OUTPUT is provided, this parameter must not be NONE.")
public picard.util.IntervalListTools.Output OUTPUT_VALUE

COUNT_OUTPUT

@Argument(doc="File to which to print count of bases or intervals in final output interval list.  When not set, value indicated by OUTPUT_VALUE will be printed to stdout.  If this parameter is set, OUTPUT_VALUE must not be NONE.",
          optional=true)
public java.io.File COUNT_OUTPUT

Constructor Detail

IntervalListTools

public IntervalListTools()

Method Detail

doWork

protected int doWork()

Description copied from class: CommandLineProgram

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.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.