org.broadinstitute.hellbender.utils

Enum NGSPlatform

java.lang.Object

java.lang.Enum<NGSPlatform>

org.broadinstitute.hellbender.utils.NGSPlatform

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<NGSPlatform>

public enum NGSPlatform
extends java.lang.Enum<NGSPlatform>

A canonical, master list of the standard NGS platforms. These values can be obtained (efficiently) from a SAMRecord object with the getNGSPlatform method.

Enum Constant Summary

Enum Constants

Enum Constant and Description
CAPILLARY
COMPLETE_GENOMICS
HELICOS
ILLUMINA
ION_TORRENT
LS454
PACBIO
SOLID
UNKNOWN

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String[]	BAM_PL_NAMES Array of the prefix names in a BAM file for each of the platforms.
protected SequencerFlowClass	sequencerType

Method Summary

Modifier and Type	Method and Description
static NGSPlatform	fromRead(GATKRead read, htsjdk.samtools.SAMFileHeader header) Convenience get -- get the NGSPlatform from a Read.
static NGSPlatform	fromReadGroupPL(java.lang.String plFromRG) Returns the NGSPlatform corresponding to the PL tag in the read group
java.lang.String	getDefaultPlatform() Returns a representative PL string for this platform
SequencerFlowClass	getSequencerType() The broad "type" of sequencer this platform represents (discrete or flow)
static boolean	isKnown(java.lang.String platform) checks whether or not the requested platform is listed in the set (and is not unknown)
static java.lang.String	knownPlatformsString() Get a human-readable list of platform names
static NGSPlatform	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static NGSPlatform[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

ILLUMINA

public static final NGSPlatform ILLUMINA

SOLID

public static final NGSPlatform SOLID

LS454

public static final NGSPlatform LS454

COMPLETE_GENOMICS

public static final NGSPlatform COMPLETE_GENOMICS

PACBIO

public static final NGSPlatform PACBIO

ION_TORRENT

public static final NGSPlatform ION_TORRENT

CAPILLARY

public static final NGSPlatform CAPILLARY

HELICOS

public static final NGSPlatform HELICOS

UNKNOWN

public static final NGSPlatform UNKNOWN

Field Detail

BAM_PL_NAMES

protected final java.lang.String[] BAM_PL_NAMES

Array of the prefix names in a BAM file for each of the platforms.

sequencerType

protected final SequencerFlowClass sequencerType

Method Detail

values

public static NGSPlatform[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (NGSPlatform c : NGSPlatform.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static NGSPlatform valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getDefaultPlatform

public final java.lang.String getDefaultPlatform()

Returns a representative PL string for this platform

Returns:

a representative PL string

getSequencerType

public final SequencerFlowClass getSequencerType()

The broad "type" of sequencer this platform represents (discrete or flow)

Returns:

a SequencerFlowClass

fromRead

public static NGSPlatform fromRead(GATKRead read,
                                   htsjdk.samtools.SAMFileHeader header)

Convenience get -- get the NGSPlatform from a Read. Just gets the platform from the read group associated with this read.

Parameters:

read - a non-null GATKRead

header - SAM header for the read

Returns:

an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match, if there is no read group for read, or there's no PL field for the read group

fromReadGroupPL

public static NGSPlatform fromReadGroupPL(java.lang.String plFromRG)

Returns the NGSPlatform corresponding to the PL tag in the read group

Parameters:

plFromRG - -- the PL field (or equivalent) in a ReadGroup object. Can be null => UNKNOWN

Returns:

an NGSPlatform object matching the PL field of the header, or UNKNOWN if there was no match or plFromRG is null

isKnown

public static boolean isKnown(java.lang.String platform)

checks whether or not the requested platform is listed in the set (and is not unknown)

Parameters:

platform - the read group string that describes the platform used. can be null

Returns:

true if the platform is known (i.e. it's in the list and is not UNKNOWN)

knownPlatformsString

public static java.lang.String knownPlatformsString()

Get a human-readable list of platform names

Returns:

the list of platform names