Modifier and Type | Field | 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 |
TODO: This is written, and 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 | Description |
---|---|
TabixFormat() |
|
TabixFormat(int flags,
int sequenceColumn,
int startPositionColumn,
int endPositionColumn,
char metaCharacter,
int numHeaderLinesToSkip) |
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