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//-----------------------------------------------------------------------------
//
// Filter parsing grammar
// Pablo Cingolani
//
//-----------------------------------------------------------------------------
grammar VcfFilter;
options {
// We're going to output an AST.
output = AST;
}
// Tokens (reserved words)
tokens {
CONDITION;
OP_BINARY;
OP_UNARY;
VAR_FIELD;
VAR_SUBFIELD;
VAR_GENOTYPE;
VAR_GENOTYPE_SUB;
VAR_EFF_SUB;
VAR_LOF_SUB;
VAR_NMD_SUB;
VAR_GENOTYPE_SUB_ARRAY;
FUNCTION_ENTRY;
FUNCTION_BOOL_GENOTYPE;
FUNCTION_BOOL_SET;
LITERAL_NUMBER;
LITERAL_STRING;
}
@lexer::header {
package ca.mcgill.mcb.pcingola.snpSift.antlr;
}
@header {
package ca.mcgill.mcb.pcingola.snpSift.antlr;
}
//-----------------------------------------------------------------------------
// Lexer
//-----------------------------------------------------------------------------
// Send runs of space and tab characters to the hidden channel.
WS : (' ' | '\t')+ { $channel = HIDDEN; };
// Treat runs of newline characters as a single NEWLINE token.
// On some platforms, newlines are represented by a \n character.
// On others they are represented by a \r and a \n character.
NEWLINE : ('\r'? '\n')+ { $channel=HIDDEN; };
// A number is a set of digits
fragment NUMBER : (DIGIT)+;
// A DIGIT
fragment DIGIT : '0'..'9' ;
// A letter
fragment LETTER : LOWER | UPPER;
fragment LOWER : 'a'..'z';
fragment UPPER : 'A'..'Z';
// Letter or digit
fragment ALPHANUM : LETTER | DIGIT;
// 'C' style single line comments
COMMENT_SL : '//' ~('\r' | '\n')* NEWLINE { $channel=HIDDEN; };
// FLOAT number (float/double) without any signNUMBER
FLOAT : ('+'|'-')? NUMBER ( '.' NUMBER )? (('e'|'E') ('+'|'-')? NUMBER)? ;
// A string literal
STRING: '\'' ~( '\n' | '\r' | '\'' )* '\'' { setText(getText().substring( 1, getText().length()-1 ) ); } ;
// An identifier.
ID : (ALPHANUM | '_' | '.' )*;
//-----------------------------------------------------------------------------
// Parser
//-----------------------------------------------------------------------------
// FCL file may contain several funcion blocks
main : f=condition -> ^(CONDITION $f);
condition : subcondition (boolOperator^ subcondition)*;
subcondition : ('!'^)? (bare | paren);
bare : unaryExpr | binaryExpr | functionBoolean ;
paren : '('! condition ')'!;
// Operations always are in parenthesis
binaryExpr : l=expression o=binOperator r=expression -> ^(OP_BINARY $o $l $r);
unaryExpr : o=uniOperator e=expression -> ^(OP_UNARY $o $e);
// All these return a boolean
boolOperator : '&' | '|';
binOperator : '=' | '>=' | '>' | '<=' | '<' | '!=' | '=~' | '!~' ;
uniOperator : '!' | 'na' | 'exists';
// Variables, functions or literals (these are values
expression : var
| functionEntry
| literalFloat
| literalString;
literalFloat : f=FLOAT -> ^(LITERAL_NUMBER $f);
literalString : s=STRING -> ^(LITERAL_STRING $s);
// Variables
var : varField | varSubfield | varGenotypeSub | varGenotypeSubArray | varEffSub | varLofSub | varNmdSub;
varField : i=ID | i='EFF' | i='LOF' | i='NMD' -> ^(VAR_FIELD $i);
varSubfield : i=ID '[' n=index ']' -> ^(VAR_SUBFIELD $i $n);
varGenotype : 'GEN' '[' g=index ']' -> ^(VAR_GENOTYPE $g);
varGenotypeSub : 'GEN' '[' g=index '].' i=ID -> ^(VAR_GENOTYPE_SUB $g $i);
varGenotypeSubArray : 'GEN' '[' g=index '].' i=ID '[' n=index ']' -> ^(VAR_GENOTYPE_SUB_ARRAY $g $i $n);
varEffSub : 'EFF' '[' g=index '].' i=ID -> ^(VAR_EFF_SUB $g $i);
varLofSub : 'LOF' '[' g=index '].' i=ID -> ^(VAR_LOF_SUB $g $i);
varNmdSub : 'NMD' '[' g=index '].' i=ID -> ^(VAR_NMD_SUB $g $i);
// Functions based on the whole VCF entry information
functionEntry : f=functionEntryName '(' ')' -> ^(FUNCTION_ENTRY $f);
functionEntryName : 'countHom' | 'countHet' | 'countVariant' | 'countRef';
// Boolean functions (return TRUE or FALSE)
functionBoolean : functionGenotypeBool
| functionBooleanSet
;
// Function on set
functionBooleanSet : e=expression f='in' 'SET' '[' i=index ']' -> ^(FUNCTION_BOOL_SET $f $i $e);
// Boolean Genotype functions (return TRUE or FALSE)
functionGenotypeBool : f=functionGenotypeBoolName '(' g=varGenotype ')' -> ^(FUNCTION_BOOL_GENOTYPE $f $g);
functionGenotypeBoolName : 'isHom' | 'isHet' | 'isVariant' | 'isRef';
// You can use '*' for 'any'
index : FLOAT | '*' | 'ANY' | '?' | 'ALL';
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