htsjdk.samtools.util

Class FileExtensions

java.lang.Object

htsjdk.samtools.util.FileExtensions

public final class FileExtensions
extends java.lang.Object

Contains file extension constants for read, alignment, and variant files

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BAI_INDEX
static java.lang.String	BAM
static java.lang.String	BCF
static java.lang.String	BED
static java.util.Set<java.lang.String>	BLOCK_COMPRESSED
static java.lang.String	COMPRESSED_VCF
static java.lang.String	COMPRESSED_VCF_INDEX
static java.lang.String	CRAM
static java.lang.String	CRAM_INDEX
static java.lang.String	CSI
static java.lang.String	DICT
static java.util.Set<java.lang.String>	FASTA extensions for read files and related formats.
static java.lang.String	FASTA_INDEX
static java.lang.String	GZI
static java.lang.String	INTERVAL_LIST
static java.lang.String	SAM extensions for alignment files SAM, BAM, CRAM.
static java.lang.String	SBI
static java.lang.String	TABIX_INDEX
static java.lang.String	TRIBBLE_INDEX
static java.lang.String	VCF extensions for VCF files and related formats.
static java.lang.String	VCF_INDEX
static java.util.List<java.lang.String>	VCF_LIST

Constructor Summary

Constructors

Constructor and Description
FileExtensions()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

FASTA

public static final java.util.Set<java.lang.String> FASTA

extensions for read files and related formats.

FASTA_INDEX

public static final java.lang.String FASTA_INDEX

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Constant Field Values

SAM

public static final java.lang.String SAM

extensions for alignment files SAM, BAM, CRAM.

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Constant Field Values

BAM

public static final java.lang.String BAM

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Constant Field Values

BAI_INDEX

public static final java.lang.String BAI_INDEX

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Constant Field Values

CRAM

public static final java.lang.String CRAM

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Constant Field Values

CRAM_INDEX

public static final java.lang.String CRAM_INDEX

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Constant Field Values

BED

public static final java.lang.String BED

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Constant Field Values

TABIX_INDEX

public static final java.lang.String TABIX_INDEX

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Constant Field Values

TRIBBLE_INDEX

public static final java.lang.String TRIBBLE_INDEX

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Constant Field Values

VCF

public static final java.lang.String VCF

extensions for VCF files and related formats.

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Constant Field Values

VCF_INDEX

public static final java.lang.String VCF_INDEX

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Constant Field Values

BCF

public static final java.lang.String BCF

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Constant Field Values

COMPRESSED_VCF

public static final java.lang.String COMPRESSED_VCF

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Constant Field Values

COMPRESSED_VCF_INDEX

public static final java.lang.String COMPRESSED_VCF_INDEX

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Constant Field Values

VCF_LIST

public static final java.util.List<java.lang.String> VCF_LIST

INTERVAL_LIST

public static final java.lang.String INTERVAL_LIST

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Constant Field Values

DICT

public static final java.lang.String DICT

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Constant Field Values

GZI

public static final java.lang.String GZI

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Constant Field Values

SBI

public static final java.lang.String SBI

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Constant Field Values

CSI

public static final java.lang.String CSI

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Constant Field Values

BLOCK_COMPRESSED

public static final java.util.Set<java.lang.String> BLOCK_COMPRESSED

Constructor Detail

FileExtensions

public FileExtensions()