org.dishevelled.bio.tools

Class WithReadGroup

java.lang.Object

org.dishevelled.bio.tools.WithReadGroup

All Implemented Interfaces:

Callable<Integer>

Direct Known Subclasses:

FastqToBam, InterleavedFastqToBam

abstract class WithReadGroup
extends Object
implements Callable<Integer>

Abstract callable with read group.

Since:

2.1

Author:

Michael Heuer

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	WithReadGroup(String readGroupId, String readGroupSample, String readGroupLibrary, String readGroupPlatformUnit, Integer readGroupInsertSize, List<String> readGroupBarcodes) Create a new callable with a read group with the specified annotations.

Method Summary

Modifier and Type	Method and Description
(package private) static StringListArgument	createReadGroupBarcodesArgument() Create and return a new read group barcodes commandline argument.
(package private) static StringArgument	createReadGroupIdArgument() Create and return a new read group id commandline argument.
(package private) static IntegerArgument	createReadGroupInsertSizeArgument() Create and return a new read group insert size commandline argument.
(package private) static StringArgument	createReadGroupLibraryArgument() Create and return a new read group library commandline argument.
(package private) static StringArgument	createReadGroupPlatformUnitArgument() Create and return a new read group platform unit commandline argument.
(package private) static StringArgument	createReadGroupSampleArgument() Create and return a new read group sample commandline argument.
protected List<String>	getReadGroupBarcodes() Return the list of read group barcodes, if any.
protected String	getReadGroupId() Return the read group id, if any.
protected Integer	getReadGroupInsertSize() Return the read group insert size, if any.
protected String	getReadGroupLibrary() Return the read group library, if any.
protected String	getReadGroupPlatformUnit() Return the read group platform unit, if any.
protected String	getReadGroupSample() Return the read group sample, if any.
protected htsjdk.samtools.SAMReadGroupRecord	toReadGroup() Create and return a new read group.
protected Optional<htsjdk.samtools.SAMReadGroupRecord>	toReadGroupOpt() Create and return an optional wrapping the read group, if any.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.concurrent.Callable

call

Constructor Detail

WithReadGroup

protected WithReadGroup(@Nullable
                        String readGroupId,
                        @Nullable
                        String readGroupSample,
                        @Nullable
                        String readGroupLibrary,
                        @Nullable
                        String readGroupPlatformUnit,
                        @Nullable
                        Integer readGroupInsertSize,
                        @Nullable
                        List<String> readGroupBarcodes)

Create a new callable with a read group with the specified annotations.

Parameters:

readGroupId - read group id, if any

readGroupSample - read group sample, if any

readGroupLibrary - read group library, if any

readGroupPlatformUnit - read group platform unit, if any

readGroupInsertSize - read group insert size, if any

readGroupBarcodes - read group barcodes, if any

Method Detail

toReadGroup

protected final htsjdk.samtools.SAMReadGroupRecord toReadGroup()

Create and return a new read group.

Returns:

a new read group

toReadGroupOpt

protected final Optional<htsjdk.samtools.SAMReadGroupRecord> toReadGroupOpt()

Create and return an optional wrapping the read group, if any.

Returns:

an optional wrapping the read group, if any

getReadGroupId

protected final String getReadGroupId()

Return the read group id, if any.

Returns:

the read group id, if any

getReadGroupSample

protected final String getReadGroupSample()

Return the read group sample, if any.

Returns:

the read group sample, if any

getReadGroupLibrary

protected final String getReadGroupLibrary()

Return the read group library, if any.

Returns:

the read group library, if any

getReadGroupPlatformUnit

protected final String getReadGroupPlatformUnit()

Return the read group platform unit, if any.

Returns:

the read group platform unit, if any

getReadGroupInsertSize

protected final Integer getReadGroupInsertSize()

Return the read group insert size, if any.

Returns:

the read group insert size, if any

getReadGroupBarcodes

protected final List<String> getReadGroupBarcodes()

Return the list of read group barcodes, if any.

Returns:

the list of read group barcodes, if any

createReadGroupIdArgument

static StringArgument createReadGroupIdArgument()

Create and return a new read group id commandline argument.

Returns:

a new read group id commandline argument

createReadGroupSampleArgument

static StringArgument createReadGroupSampleArgument()

Create and return a new read group sample commandline argument.

Returns:

a new read group sample commandline argument

createReadGroupLibraryArgument

static StringArgument createReadGroupLibraryArgument()

Create and return a new read group library commandline argument.

Returns:

a new read group library commandline argument

createReadGroupPlatformUnitArgument

static StringArgument createReadGroupPlatformUnitArgument()

Create and return a new read group platform unit commandline argument.

Returns:

a new read group platform unit commandline argument

createReadGroupInsertSizeArgument

static IntegerArgument createReadGroupInsertSizeArgument()

Create and return a new read group insert size commandline argument.

Returns:

a new read group insert size commandline argument

createReadGroupBarcodesArgument

static StringListArgument createReadGroupBarcodesArgument()

Create and return a new read group barcodes commandline argument.

Returns:

a new read group barcodes commandline argument