public class TabixFormat
extends java.lang.Object
implements java.lang.Cloneable
Modifier and Type | Field and Description |
---|---|
static 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 int |
GENERIC_FLAGS |
static TabixFormat |
GFF
Predefined headers for known formats
|
char |
metaCharacter
Lines in the file being indexed that start with this character are ignored.
|
int |
numHeaderLinesToSkip
This is part of the index header, but does not appear to be used.
|
static TabixFormat |
PSLTBL |
static TabixFormat |
SAM |
static 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 int |
UCSC_FLAGS |
static TabixFormat |
VCF |
static int |
VCF_FLAGS |
static int |
ZERO_BASED |
Constructor and Description |
---|
TabixFormat() |
TabixFormat(int flags,
int sequenceColumn,
int startPositionColumn,
int endPositionColumn,
char metaCharacter,
int numHeaderLinesToSkip) |
Modifier and Type | Method and Description |
---|---|
TabixFormat |
clone() |
boolean |
equals(java.lang.Object o) |
int |
hashCode() |
public static final int ZERO_BASED
public static final int GENERIC_FLAGS
public static final int SAM_FLAGS
public static final int VCF_FLAGS
public static final int UCSC_FLAGS
public static TabixFormat GFF
public static TabixFormat BED
public static TabixFormat PSLTBL
public static TabixFormat SAM
public static TabixFormat VCF
public int flags
public int sequenceColumn
public int startPositionColumn
public int endPositionColumn
public char metaCharacter
public int numHeaderLinesToSkip
public TabixFormat()
public TabixFormat(int flags, int sequenceColumn, int startPositionColumn, int endPositionColumn, char metaCharacter, int numHeaderLinesToSkip)
public TabixFormat clone()
clone
in class java.lang.Object
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object