org.broadinstitute.hellbender.engine

Class GATKPath

java.lang.Object

htsjdk.io.HtsPath

org.broadinstitute.hellbender.engine.GATKPath

All Implemented Interfaces:

htsjdk.io.IOPath, java.io.Serializable, org.broadinstitute.barclay.argparser.TaggedArgument

Direct Known Subclasses:

FeatureInput

public class GATKPath
extends htsjdk.io.HtsPath
implements org.broadinstitute.barclay.argparser.TaggedArgument, java.io.Serializable

GATK tool command line arguments that are input or output resources. These can have an optional name supplied on the command line, as well as one or more optional tag/value pairs.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	HDFS_SCHEME

Constructor Summary

Constructors

Constructor and Description
GATKPath(GATKPath sourceGATKPath) Create a GATKPath from an existing GATKPath.
GATKPath(java.lang.String uriString) The raw value for this specifier as provided by the user.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
java.io.InputStream	getInputStream()
java.io.OutputStream	getOutputStream() Open a path for writing regardless of whether it's on GCS, HDFS or local disk.
java.lang.String	getTag()
java.util.Map<java.lang.String,java.lang.String>	getTagAttributes()
int	hashCode()
boolean	isHadoopURL() Returns true if this is a HDFS (Hadoop filesystem) URL.
void	setTag(java.lang.String tagName)
void	setTagAttributes(java.util.Map<java.lang.String,java.lang.String> attributes)
java.nio.file.Path	toPath()
java.lang.String	toString()

Methods inherited from class htsjdk.io.HtsPath

getCachedPath, getRawInputString, getToPathFailureReason, getURI, getURIString, hasFileSystemProvider, isPath, setCachedPath

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.io.IOPath

getBaseName, getExtension, getScheme, hasExtension, isBam, isCram, isFasta, isSam

Field Detail

HDFS_SCHEME

public static final java.lang.String HDFS_SCHEME

See Also:

Constant Field Values

Constructor Detail

GATKPath

public GATKPath(java.lang.String uriString)

The raw value for this specifier as provided by the user. Can be a local file or valid URI.

Parameters:

uriString -

GATKPath

public GATKPath(GATKPath sourceGATKPath)

Create a GATKPath from an existing GATKPath. Propagates tag and tag attributes.

Parameters:

sourceGATKPath -

Method Detail

toPath

public java.nio.file.Path toPath()

Specified by:

toPath in interface htsjdk.io.IOPath

Overrides:

toPath in class htsjdk.io.HtsPath

getInputStream

public java.io.InputStream getInputStream()

Specified by:

getInputStream in interface htsjdk.io.IOPath

Overrides:

getInputStream in class htsjdk.io.HtsPath

getOutputStream

public java.io.OutputStream getOutputStream()

Open a path for writing regardless of whether it's on GCS, HDFS or local disk. For writing to GCS it'll use the application/octet-stream MIME type.

Specified by:

getOutputStream in interface htsjdk.io.IOPath

Overrides:

getOutputStream in class htsjdk.io.HtsPath

Returns:

an OutputStream that writes to the path specified by this UR.

isHadoopURL

public boolean isHadoopURL()

Returns true if this is a HDFS (Hadoop filesystem) URL.

setTag

public void setTag(java.lang.String tagName)

Specified by:

setTag in interface org.broadinstitute.barclay.argparser.TaggedArgument

getTag

public java.lang.String getTag()

Specified by:

getTag in interface org.broadinstitute.barclay.argparser.TaggedArgument

setTagAttributes

public void setTagAttributes(java.util.Map<java.lang.String,java.lang.String> attributes)

Specified by:

setTagAttributes in interface org.broadinstitute.barclay.argparser.TaggedArgument

getTagAttributes

public java.util.Map<java.lang.String,java.lang.String> getTagAttributes()

Specified by:

getTagAttributes in interface org.broadinstitute.barclay.argparser.TaggedArgument

toString

public java.lang.String toString()

Overrides:

toString in class htsjdk.io.HtsPath

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class htsjdk.io.HtsPath

hashCode

public int hashCode()

Overrides:

hashCode in class htsjdk.io.HtsPath