org.broadinstitute.hellbender.utils.codecs.gtf

Enum GencodeGtfFeature.RemapStatus

java.lang.Object

java.lang.Enum<GencodeGtfFeature.RemapStatus>

org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.RemapStatus

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<GencodeGtfFeature.RemapStatus>

Enclosing class:

GencodeGtfFeature

public static enum GencodeGtfFeature.RemapStatus
extends java.lang.Enum<GencodeGtfFeature.RemapStatus>

Attribute that indicates the status of the mapping. For more information, see: https://www.gencodegenes.org/data_format.html https://en.wikipedia.org/wiki/General_feature_format http://www.gencodegenes.org/releases/grch37_mapped_releases.html#attrib

Enum Constant Summary

Enum Constants

Enum Constant and Description
AUTOMATIC_GENE Gene is from an automatic process (ENSEMBL source).
AUTOMATIC_SMALL_NCRNA_GENE Gene is from a small, automatic (ENSEMBL source) non-coding RNA.
DELETED Gene or transcript did not map to the target genome.
FULL_CONTIG Gene or transcript completely mapped to the target genome with all features intact.
FULL_FRAGMENT Gene or transcript completely mapped to the target genome with insertions in some features.
GENE_CONFLICT Transcripts in the gene mapped to multiple locations.
GENE_SIZE_CHANGE Transcripts caused gene length to change by more than 50%.
NO_SEQ_MAP The source sequence is not in the assembly alignments.
PARTIAL Gene or transcript partially mapped to the target genome.
PSEUDOGENE Pseudogene annotations (excluding polymorphic).

Method Summary

Modifier and Type	Method and Description
static GencodeGtfFeature.RemapStatus	getEnum(java.lang.String s)
java.lang.String	toString()
static GencodeGtfFeature.RemapStatus	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static GencodeGtfFeature.RemapStatus[]	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, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

FULL_CONTIG

public static final GencodeGtfFeature.RemapStatus FULL_CONTIG

Gene or transcript completely mapped to the target genome with all features intact.

FULL_FRAGMENT

public static final GencodeGtfFeature.RemapStatus FULL_FRAGMENT

Gene or transcript completely mapped to the target genome with insertions in some features. These are usually small insertions.

PARTIAL

public static final GencodeGtfFeature.RemapStatus PARTIAL

Gene or transcript partially mapped to the target genome.

DELETED

public static final GencodeGtfFeature.RemapStatus DELETED

Gene or transcript did not map to the target genome.

NO_SEQ_MAP

public static final GencodeGtfFeature.RemapStatus NO_SEQ_MAP

The source sequence is not in the assembly alignments. This will occur with alt loci genes if the alignments only contain the primary assembly.

GENE_CONFLICT

public static final GencodeGtfFeature.RemapStatus GENE_CONFLICT

Transcripts in the gene mapped to multiple locations.

GENE_SIZE_CHANGE

public static final GencodeGtfFeature.RemapStatus GENE_SIZE_CHANGE

Transcripts caused gene length to change by more than 50%. This is to detect mapping to processed pseudogenes and mapping across tandem gene duplications.

AUTOMATIC_SMALL_NCRNA_GENE

public static final GencodeGtfFeature.RemapStatus AUTOMATIC_SMALL_NCRNA_GENE

Gene is from a small, automatic (ENSEMBL source) non-coding RNA. Taken from the target annotation.

AUTOMATIC_GENE

public static final GencodeGtfFeature.RemapStatus AUTOMATIC_GENE

Gene is from an automatic process (ENSEMBL source). Taken from the target annotation.

PSEUDOGENE

public static final GencodeGtfFeature.RemapStatus PSEUDOGENE

Pseudogene annotations (excluding polymorphic).

Method Detail

values

public static GencodeGtfFeature.RemapStatus[] 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 (GencodeGtfFeature.RemapStatus c : GencodeGtfFeature.RemapStatus.values())
    System.out.println(c);

Returns:

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

valueOf

public static GencodeGtfFeature.RemapStatus 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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Enum<GencodeGtfFeature.RemapStatus>

getEnum

public static GencodeGtfFeature.RemapStatus getEnum(java.lang.String s)