org.broadinstitute.hellbender.cmdline.argumentcollections

Class IntervalArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

OptionalIntervalArgumentCollection, RequiredIntervalArgumentCollection

public abstract class IntervalArgumentCollection
extends java.lang.Object
implements java.io.Serializable

Intended to be used as an @ArgumentCollection for specifying intervals at the command line. Subclasses must override getIntervalStrings and addToIntervalStrings().

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EXCLUDE_INTERVALS_LONG_NAME
static java.lang.String	EXCLUDE_INTERVALS_SHORT_NAME
protected java.util.List<java.lang.String>	excludeIntervalStrings Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite).
static java.lang.String	INTERVAL_EXCLUSION_PADDING_LONG_NAME
static java.lang.String	INTERVAL_MERGING_RULE_LONG_NAME
static java.lang.String	INTERVAL_PADDING_LONG_NAME
static java.lang.String	INTERVAL_SET_RULE_LONG_NAME
protected int	intervalExclusionPadding Use this to add padding to the intervals specified using -XL.
protected IntervalMergingRule	intervalMergingRule By default, the program merges abutting intervals (i.e.
protected int	intervalPadding Use this to add padding to the intervals specified using -L.
protected IntervalSetRule	intervalSetRule By default, the program will take the UNION of all intervals specified using -L and/or -XL.
protected TraversalParameters	traversalParameters Full parameters for traversal, including our parsed intervals and a flag indicating whether unmapped records should be returned.

Constructor Summary

Constructors

Constructor and Description
IntervalArgumentCollection()

Method Summary

Modifier and Type	Method and Description
protected abstract void	addToIntervalStrings(java.lang.String newInterval) Add an extra interval string to the intervals to include.
int	getIntervalExclusionPadding() Get the interval exclusion padding specified on the command line.
IntervalMergingRule	getIntervalMergingRule() Get the interval merging rule specified on the command line.
int	getIntervalPadding() Get the interval padding specified on the command line.
java.util.List<SimpleInterval>	getIntervals(htsjdk.samtools.SAMSequenceDictionary sequenceDict) Get the intervals specified on the command line.
IntervalSetRule	getIntervalSetRule() Get the interval set rule specified on the command line.
protected abstract java.util.List<java.lang.String>	getIntervalStrings() Subclasses must provide a -L argument and override this to return the results of that argument.
java.util.List<SimpleInterval>	getIntervalsWithoutMerging(htsjdk.samtools.SAMSequenceDictionary sequenceDict) Returns the full set of traversal intervals specified on the command line, including parsed intervals without merging intervals specified by the user on the command line.
TraversalParameters	getTraversalParameters(htsjdk.samtools.SAMSequenceDictionary sequenceDict) Returns the full set of traversal parameters specified on the command line, including the parsed intervals and a flag indicating whether unmapped records were requested.
boolean	intervalsSpecified() Have any intervals been specified for inclusion or exclusion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EXCLUDE_INTERVALS_LONG_NAME

public static final java.lang.String EXCLUDE_INTERVALS_LONG_NAME

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Constant Field Values

EXCLUDE_INTERVALS_SHORT_NAME

public static final java.lang.String EXCLUDE_INTERVALS_SHORT_NAME

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Constant Field Values

INTERVAL_SET_RULE_LONG_NAME

public static final java.lang.String INTERVAL_SET_RULE_LONG_NAME

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Constant Field Values

INTERVAL_PADDING_LONG_NAME

public static final java.lang.String INTERVAL_PADDING_LONG_NAME

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Constant Field Values

INTERVAL_EXCLUSION_PADDING_LONG_NAME

public static final java.lang.String INTERVAL_EXCLUSION_PADDING_LONG_NAME

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Constant Field Values

INTERVAL_MERGING_RULE_LONG_NAME

public static final java.lang.String INTERVAL_MERGING_RULE_LONG_NAME

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Constant Field Values

excludeIntervalStrings

@Argument(fullName="exclude-intervals",
          shortName="XL",
          doc="One or more genomic intervals to exclude from processing",
          suppressFileExpansion=true,
          optional=true,
          common=true)
protected final java.util.List<java.lang.String> excludeIntervalStrings

Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals).

intervalSetRule

@Argument(fullName="interval-set-rule",
          shortName="isr",
          doc="Set merging approach to use for combining interval inputs",
          common=true)
protected IntervalSetRule intervalSetRule

By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

intervalPadding

@Argument(fullName="interval-padding",
          shortName="ip",
          doc="Amount of padding (in bp) to add to each interval you are including.",
          common=true)
protected int intervalPadding

Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

intervalExclusionPadding

@Argument(fullName="interval-exclusion-padding",
          shortName="ixp",
          doc="Amount of padding (in bp) to add to each interval you are excluding.",
          common=true)
protected int intervalExclusionPadding

Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

intervalMergingRule

@Argument(fullName="interval-merging-rule",
          shortName="imr",
          doc="Interval merging rule for abutting intervals",
          optional=true)
protected IntervalMergingRule intervalMergingRule

By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

traversalParameters

protected TraversalParameters traversalParameters

Full parameters for traversal, including our parsed intervals and a flag indicating whether unmapped records should be returned. Lazily initialized.

Constructor Detail

IntervalArgumentCollection

public IntervalArgumentCollection()

Method Detail

getIntervalStrings

protected abstract java.util.List<java.lang.String> getIntervalStrings()

Subclasses must provide a -L argument and override this to return the results of that argument. The -L argument specifies intervals to include in analysis and has the following semantics It can use samtools-style intervals either explicitly on the command line (e.g. -L 1 or -L 1:100-200) or by loading in a file containing a list of intervals (e.g. -L myFile.intervals). It can be specified multiple times.

Returns:

string gathered from the command line -L argument to be parsed into intervals to include

addToIntervalStrings

protected abstract void addToIntervalStrings(java.lang.String newInterval)

Add an extra interval string to the intervals to include. ONLY for testing -- will throw if called after interval parsing has been performed.

getIntervals

public java.util.List<SimpleInterval> getIntervals(htsjdk.samtools.SAMSequenceDictionary sequenceDict)

Get the intervals specified on the command line.

Parameters:

sequenceDict - used to validate intervals

Returns:

a list of the given intervals after processing and validation

getIntervalSetRule

public IntervalSetRule getIntervalSetRule()

Get the interval set rule specified on the command line.

getIntervalPadding

public int getIntervalPadding()

Get the interval padding specified on the command line.

getIntervalExclusionPadding

public int getIntervalExclusionPadding()

Get the interval exclusion padding specified on the command line.

getIntervalMergingRule

public IntervalMergingRule getIntervalMergingRule()

Get the interval merging rule specified on the command line.

getIntervalsWithoutMerging

public java.util.List<SimpleInterval> getIntervalsWithoutMerging(htsjdk.samtools.SAMSequenceDictionary sequenceDict)

Returns the full set of traversal intervals specified on the command line, including parsed intervals without merging intervals specified by the user on the command line. This is an advanced use case NOTE: this currently does not account for interval exclusion arguments

Parameters:

sequenceDict - used to validate intervals

Returns:

the full set of intervals specified on the command line, without any merging performed

getTraversalParameters

public TraversalParameters getTraversalParameters(htsjdk.samtools.SAMSequenceDictionary sequenceDict)

Returns the full set of traversal parameters specified on the command line, including the parsed intervals and a flag indicating whether unmapped records were requested.

Parameters:

sequenceDict - used to validate intervals

Returns:

the full set of traversal parameters specified on the command line

intervalsSpecified

public boolean intervalsSpecified()

Have any intervals been specified for inclusion or exclusion