Package htsjdk.tribble.index.tabix
Class TabixFormat
- java.lang.Object
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- htsjdk.tribble.index.tabix.TabixFormat
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Field Summary
Fields 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 formatschar
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 nameint
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
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Constructor Summary
Constructors Constructor Description TabixFormat()
TabixFormat(int flags, int sequenceColumn, int startPositionColumn, int endPositionColumn, char metaCharacter, int numHeaderLinesToSkip)
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Field Detail
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ZERO_BASED
public static final int ZERO_BASED
- See Also:
- Constant Field Values
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GENERIC_FLAGS
public static final int GENERIC_FLAGS
- See Also:
- Constant Field Values
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SAM_FLAGS
public static final int SAM_FLAGS
- See Also:
- Constant Field Values
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VCF_FLAGS
public static final int VCF_FLAGS
- See Also:
- Constant Field Values
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UCSC_FLAGS
public static final int UCSC_FLAGS
- See Also:
- Constant Field Values
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GFF
public static final TabixFormat GFF
Predefined headers for known formats
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BED
public static final TabixFormat BED
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PSLTBL
public static final TabixFormat PSLTBL
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SAM
public static final TabixFormat SAM
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VCF
public static final TabixFormat VCF
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flags
public int flags
Describes interpretation of file being indexed. See FLAGS constants above.
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sequenceColumn
public int sequenceColumn
One-based index of the column in the file being indexed containing the sequence name
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startPositionColumn
public int startPositionColumn
One-based index of the column in the file being indexed containing the start position.
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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.
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metaCharacter
public char metaCharacter
Lines in the file being indexed that start with this character are ignored.
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numHeaderLinesToSkip
public int numHeaderLinesToSkip
TODO: This is written, and part of the index header, but does not appear to be used.
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