Package htsjdk.tribble.index.tabix

Class TabixFormat

java.lang.Object

htsjdk.tribble.index.tabix.TabixFormat

All Implemented Interfaces:

Cloneable

public class TabixFormat
extends Object
implements Cloneable

The values in a Tabix header that define the format of the file being indexed, e.g. gff, bed, vcf

Field Summary

Fields

Modifier and Type	Field	Description
static final TabixFormat	BED
int	endPositionColumn	One-based index of the column in the file being indexed containing the end position.
int	flags	Describes interpretation of file being indexed.
static final int	GENERIC_FLAGS
static final TabixFormat	GFF	Predefined headers for known formats
char	metaCharacter	Lines in the file being indexed that start with this character are ignored.
int	numHeaderLinesToSkip	TODO: This is written, and part of the index header, but does not appear to be used.
static final TabixFormat	PSLTBL
static final TabixFormat	SAM
static final int	SAM_FLAGS
int	sequenceColumn	One-based index of the column in the file being indexed containing the sequence name
int	startPositionColumn	One-based index of the column in the file being indexed containing the start position.
static final int	UCSC_FLAGS
static final TabixFormat	VCF
static final int	VCF_FLAGS
static final int	ZERO_BASED

Constructor Summary

Constructors

Constructor	Description
TabixFormat()
TabixFormat(int flags, int sequenceColumn, int startPositionColumn, int endPositionColumn, char metaCharacter, int numHeaderLinesToSkip)

Method Summary

Modifier and Type	Method	Description
TabixFormat	clone()
boolean	equals(Object o)
int	hashCode()

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Details

ZERO_BASED

public static final int ZERO_BASED

See Also:

• Constant Field Values

GENERIC_FLAGS

public static final int GENERIC_FLAGS

See Also:

• Constant Field Values

SAM_FLAGS

public static final int SAM_FLAGS

See Also:

• Constant Field Values

VCF_FLAGS

public static final int VCF_FLAGS

See Also:

• Constant Field Values

UCSC_FLAGS

public static final int UCSC_FLAGS

See Also:

• Constant Field Values

GFF

public static final TabixFormat GFF

Predefined headers for known formats

BED

public static final TabixFormat BED

PSLTBL

public static final TabixFormat PSLTBL

SAM

public static final TabixFormat SAM

VCF

public static final TabixFormat VCF

flags

public int flags

Describes interpretation of file being indexed. See FLAGS constants above.

sequenceColumn

public int sequenceColumn

One-based index of the column in the file being indexed containing the sequence name

startPositionColumn

public int startPositionColumn

One-based index of the column in the file being indexed containing the start position.

endPositionColumn

public int endPositionColumn

One-based index of the column in the file being indexed containing the end position. Zero implies there is no end position column.

metaCharacter

public char metaCharacter

Lines in the file being indexed that start with this character are ignored.

numHeaderLinesToSkip

public int numHeaderLinesToSkip

TODO: This is written, and part of the index header, but does not appear to be used.

Constructor Details

TabixFormat

public TabixFormat()

TabixFormat

public TabixFormat(int flags,
 int sequenceColumn,
 int startPositionColumn,
 int endPositionColumn,
 char metaCharacter,
 int numHeaderLinesToSkip)

Method Details

clone

public TabixFormat clone()

Overrides:

clone in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object