pro.parseq.vcf.utils

Class VcfGrammar

java.lang.Object

pro.parseq.vcf.utils.VcfGrammar

public class VcfGrammar
extends Object

Class to hold VCF specification properties (see VCFv4.2 specification for more details)

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLELE_DELIMITER
static int	ALT_COLUMN_IDX
static int	CHROM_COLUMN_IDX
static String	COLUMN_DELIMITER
static Pattern	dataLinePattern
static Pattern	exactCountNumberValuePattern
static Pattern	fileformatPattern
static int	FILTER_COLUMN_IDX
static String	FILTER_DELIMITER
static String	FILTER_PASSED
static Pattern	filterDescriptionPattern
static Pattern	filterIdPattern
static Pattern	filterPattern
static int	FORMAT_COLUMN_IDX
static String	FORMAT_DELIMITER
static Pattern	formatDescriptionPattern
static Pattern	formatIdPattern
static Pattern	formatNumberPattern
static Pattern	formatPattern
static Pattern	formatTypePattern
static String	GENOTYPE_DELIMITER
static String	GENOTYPE_FIELD
static Pattern	genotypeFirstAllelePattern
static Pattern	genotypeSecondAllelePattern
static Pattern	genotypeUnknownFirstAllelePattern
static Pattern	genotypeUnknownSecondAllelePattern
static Pattern	genotypeValuePattern
static Pattern	headerPattern
static int	ID_COLUMN_IDX
static String	ID_DELIMITER
static int	INFO_COLUMN_IDX
static String	INFO_DELIMITER
static String	INFO_KEY_VALUE_DELIMITER
static String	INFO_VALUE_DELIMITER
static Pattern	infoDescriptionPattern
static Pattern	infoIdPattern
static Pattern	infoNumberPattern
static Pattern	infoPattern
static Pattern	infoSourcePattern
static Pattern	infoTypePattern
static Pattern	infoVersionPattern
static int	MANDATORY_COLUMNS_NUMBER
static Pattern	metadataKeyPattern
static Pattern	metadataPattern
static Pattern	metadataValuePattern
static String	MISSING_VALUE
static int	POS_COLUMN_IDX
static int	QUAL_COLUMN_IDX
static int	REF_COLUMN_IDX
static String	REFERENCE_ALLELE
static String	UNBOUNDED_VALUE
static String	VALUE_PER_ALLELE
static String	VALUE_PER_ALLELE_WITH_REF
static String	VALUE_PER_GENOTYPE

Constructor Summary

Constructors

Constructor and Description
VcfGrammar()

Method Summary

Methods inherited from class java.lang.Object

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

Field Detail

fileformatPattern

public static final Pattern fileformatPattern

metadataPattern

public static final Pattern metadataPattern

metadataKeyPattern

public static final Pattern metadataKeyPattern

metadataValuePattern

public static final Pattern metadataValuePattern

filterPattern

public static final Pattern filterPattern

filterIdPattern

public static final Pattern filterIdPattern

filterDescriptionPattern

public static final Pattern filterDescriptionPattern

formatPattern

public static final Pattern formatPattern

formatIdPattern

public static final Pattern formatIdPattern

formatNumberPattern

public static final Pattern formatNumberPattern

formatTypePattern

public static final Pattern formatTypePattern

formatDescriptionPattern

public static final Pattern formatDescriptionPattern

genotypeValuePattern

public static final Pattern genotypeValuePattern

genotypeFirstAllelePattern

public static final Pattern genotypeFirstAllelePattern

genotypeSecondAllelePattern

public static final Pattern genotypeSecondAllelePattern

genotypeUnknownFirstAllelePattern

public static final Pattern genotypeUnknownFirstAllelePattern

genotypeUnknownSecondAllelePattern

public static final Pattern genotypeUnknownSecondAllelePattern

GENOTYPE_FIELD

public static final String GENOTYPE_FIELD

See Also:

Constant Field Values

GENOTYPE_DELIMITER

public static final String GENOTYPE_DELIMITER

REFERENCE_ALLELE

public static final String REFERENCE_ALLELE

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Constant Field Values

VALUE_PER_ALLELE

public static final String VALUE_PER_ALLELE

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Constant Field Values

VALUE_PER_ALLELE_WITH_REF

public static final String VALUE_PER_ALLELE_WITH_REF

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Constant Field Values

VALUE_PER_GENOTYPE

public static final String VALUE_PER_GENOTYPE

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Constant Field Values

UNBOUNDED_VALUE

public static final String UNBOUNDED_VALUE

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Constant Field Values

infoPattern

public static final Pattern infoPattern

infoIdPattern

public static final Pattern infoIdPattern

infoNumberPattern

public static final Pattern infoNumberPattern

infoTypePattern

public static final Pattern infoTypePattern

infoDescriptionPattern

public static final Pattern infoDescriptionPattern

infoSourcePattern

public static final Pattern infoSourcePattern

infoVersionPattern

public static final Pattern infoVersionPattern

exactCountNumberValuePattern

public static final Pattern exactCountNumberValuePattern

headerPattern

public static final Pattern headerPattern

MANDATORY_COLUMNS_NUMBER

public static final int MANDATORY_COLUMNS_NUMBER

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Constant Field Values

COLUMN_DELIMITER

public static final String COLUMN_DELIMITER

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Constant Field Values

CHROM_COLUMN_IDX

public static final int CHROM_COLUMN_IDX

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Constant Field Values

POS_COLUMN_IDX

public static final int POS_COLUMN_IDX

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Constant Field Values

ID_COLUMN_IDX

public static final int ID_COLUMN_IDX

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Constant Field Values

REF_COLUMN_IDX

public static final int REF_COLUMN_IDX

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Constant Field Values

ALT_COLUMN_IDX

public static final int ALT_COLUMN_IDX

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Constant Field Values

QUAL_COLUMN_IDX

public static final int QUAL_COLUMN_IDX

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Constant Field Values

FILTER_COLUMN_IDX

public static final int FILTER_COLUMN_IDX

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Constant Field Values

INFO_COLUMN_IDX

public static final int INFO_COLUMN_IDX

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Constant Field Values

FORMAT_COLUMN_IDX

public static final int FORMAT_COLUMN_IDX

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Constant Field Values

dataLinePattern

public static final Pattern dataLinePattern

FILTER_PASSED

public static final String FILTER_PASSED

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Constant Field Values

MISSING_VALUE

public static final String MISSING_VALUE

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Constant Field Values

ALLELE_DELIMITER

public static final String ALLELE_DELIMITER

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Constant Field Values

FILTER_DELIMITER

public static final String FILTER_DELIMITER

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Constant Field Values

FORMAT_DELIMITER

public static final String FORMAT_DELIMITER

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Constant Field Values

ID_DELIMITER

public static final String ID_DELIMITER

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Constant Field Values

INFO_DELIMITER

public static final String INFO_DELIMITER

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Constant Field Values

INFO_KEY_VALUE_DELIMITER

public static final String INFO_KEY_VALUE_DELIMITER

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Constant Field Values

INFO_VALUE_DELIMITER

public static final String INFO_VALUE_DELIMITER

See Also:

Constant Field Values

Constructor Detail

VcfGrammar

public VcfGrammar()