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vcf_v43.ragel
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/**
* Copyright 2014-2017 EMBL - European Bioinformatics Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
%%{
machine vcf_v43;
include vcf "vcf.ragel";
#############################################
# Actions definition #
#############################################
########## Incorrect metadata and header actions ##########
# Fileformat line
action fileformat_error {
ErrorPolicy::handle_error(*this,
new FileformatError{n_lines, "The fileformat declaration is not 'fileformat=VCFv4.3'"});
fhold; fgoto meta_section_skip;
}
# FORMAT metadata
action meta_format_number_err {
ErrorPolicy::handle_error(*this, new MetaSectionError{n_lines, "FORMAT metadata Number is not a number, A, R, G or dot"});
fhold; fgoto meta_section_skip;
}
# INFO metadata
action meta_info_number_err {
ErrorPolicy::handle_error(*this, new MetaSectionError{n_lines, "INFO metadata Number is not a number, A, R, G or dot"});
fhold; fgoto meta_section_skip;
}
########## Incorrect records actions ##########
# Format
action format_error {
ErrorPolicy::handle_error(*this, new FormatBodyError{n_lines, "Format does not start with a letter/underscore followed by alphanumeric/underscore/dot characters"});
fhold; fgoto body_section_skip;
}
action no_newline_at_eof_error {
ErrorPolicy::handle_error(*this, new BodySectionError{n_lines, "There is no newline at the end of the file"});
fhold; fgoto body_section_skip;
}
#################################################
# Machine definition #
#################################################
## A contig must be a sequence name allowed by the SAM format ( regex [!-)+-<>-~][!-~]* ) excluding the characters <>[]:*
## A chromosome must be a string with no white-spaces or colons, and may be surrounded by < > symbols (for contigs)
meta_contig_char= alnum | ( punct - ( '<' | '>' | '[' | ']' | '*' | '=' | ',' ) ) ;
chrom_basic = (meta_contig_char - '#') (meta_contig_char)* ;
chrom_contig = '<' chrom_basic '>' ;
chromosome = chrom_basic | chrom_contig ;
# File format line
fileformat_name = 'VCFv4.3' >token_begin $token_middle %fileformat_end $err(fileformat_error) ;
fileformat = '##fileformat=' fileformat_name ;
# Meta-data
meta_typeid = ( ( print - '=' )+ - ('ALT' | 'FILTER' | 'FORMAT' | 'INFO' | 'assembly' | 'contig' | 'META' | 'SAMPLE' | 'PEDIGREE' | 'pedigreeDB') ) >token_begin @token_middle %meta_typeid_generic ;
meta_key = ( (alnum | '.' | '_' | '-' )+ - (punct)+ ) >token_begin @token_middle %meta_key_generic;
## A value can be expressed in multiple ways:
## - The line is a single key-value pair (meta_value): the value cannot start with an angle bracket, quote or linebreak, but it is free text thereafter
## - One of multiple key-value pairs, non-quoted (meta_field_value): the value cannot contain a comma -end of field-, or a closing angle bracket -end of entry-, or quote
## - One of multiple key-value pairs, quoted (meta_field_desc): the value can contain any character except for non-escaped quotes
meta_value = ((print - ('<' | '"' | NL)) (print)*) >token_begin $token_middle %token_end ;
meta_field_value= (print - (',' | '>' | '"'))+ >token_begin $token_middle %token_end ;
meta_field_desc = (('\\' print) | (print - '"'))* >token_begin $token_middle %token_end ;
meta_values = ('"' meta_field_desc '"') | meta_field_value ;
meta_field = meta_key '=' meta_values ;
meta_field_num = ( (digit)+ | 'A' | 'R' | 'G' | '.' ) >token_begin @token_middle %token_end ;
meta_field_type = (alpha)+ >token_begin @token_middle %token_end ;
meta_alt = 'ID=' %meta_id alt_id >token_begin @token_middle %token_end $err(meta_alt_id_err)
',Description=' %meta_description '"' meta_field_desc '"' $err(meta_desc_err)
(',' identifier $err(meta_id_err) '="' meta_field_desc '"' $err(meta_desc_err))* ;
meta_assembly = url $err(meta_url_err) ;
meta_contig = 'ID=' %meta_id chrom_basic >token_begin $token_middle %token_end $err(meta_id_err)
(',' identifier '=' meta_values)* ;
meta_filter = 'ID=' %meta_id identifier $err(meta_id_err)
',Description=' %meta_description '"' meta_field_desc '"' $err(meta_desc_err)
(',' identifier $err(meta_id_err) '="' meta_field_desc '"' $err(meta_desc_err))* ;
meta_format = 'ID=' %meta_id identifier $err(meta_id_err)
',Number=' %meta_number meta_field_num $err(meta_format_number_err)
',Type=' %meta_type meta_field_type $err(meta_info_type_err)
',Description=' %meta_description '"' meta_field_desc '"' $err(meta_desc_err)
(',' identifier $err(meta_id_err) '="' meta_field_desc '"' $err(meta_desc_err))* ;
meta_info = 'ID=' %meta_id identifier $err(meta_id_err)
',Number=' %meta_number meta_field_num $err(meta_info_number_err)
',Type=' %meta_type meta_field_type $err(meta_info_type_err)
',Description=' %meta_description '"' meta_field_desc '"' $err(meta_desc_err)
(',' identifier $err(meta_id_err) '="' meta_field_desc '"' $err(meta_desc_err))* ;
## 3 different ways to define a PEDIGREE tag now:
## ID=TumourSample,Original=GermlineID
## ID=ChildID,Father=FatherID,Mother=MotherID
## ID=SampleID,Name_1=Ancestor_1,...,Name_N=Ancestor_N
meta_pedigree_name = ('Name_' (digit)+) >token_begin $token_middle %token_end;
meta_pedigree = 'ID=' %meta_id identifier $err(meta_id_err)
(
( ',Original=' %meta_original identifier $err(meta_pedigree_original_err) ) |
( ',Father=' %meta_father identifier $err(meta_pedigree_parents_err)
',Mother=' %meta_mother identifier $err(meta_pedigree_parents_err) ) |
(',' meta_pedigree_name $err(meta_pedigree_names_err) '=' identifier $err(meta_pedigree_names_err))+
) ;
meta_pedigreeDB = url $err(meta_url_err) ;
## META values don't seem to have any particular restrictions so just applying those critical for parsing
meta_meta_value = (print - (',' | '<' | '>' | space))+ ;
meta_meta_values = (meta_meta_value (',' (space)? meta_meta_value)*) >token_begin $token_middle %token_end ;
meta_meta = 'ID=' %meta_id identifier $err(meta_id_err)
',Number=' %meta_number '.' $err(meta_meta_number_err)
',Type=' %meta_type 'String' $err(meta_meta_type_err)
',Values=' %meta_values '[' meta_meta_values ']' $err(meta_meta_values_err) ;
## Multiple ways to describe a sample now
meta_sample = 'ID=' %meta_id identifier $err(meta_id_err)
(',' identifier '=' meta_values)* ;
meta_entry = '##' (
('ALT' %meta_typeid_alt '=<' meta_alt '>' ) $err(meta_alt_err) |
('FILTER' %meta_typeid_filter '=<' meta_filter '>' ) $err(meta_filter_err) |
('FORMAT' %meta_typeid_format '=<' meta_format '>' ) $err(meta_format_err) |
('INFO' %meta_typeid_info '=<' meta_info '>' ) $err(meta_info_err) |
('assembly' %meta_typeid_assembly '=' meta_assembly ) $err(meta_assembly_err) |
('contig' %meta_typeid_contig '=<' meta_contig '>' ) $err(meta_contig_err) |
('META' %meta_typeid_meta '=<' meta_meta '>' ) $err(meta_meta_err) |
('SAMPLE' %meta_typeid_sample '=<' meta_sample '>' ) $err(meta_sample_err) |
('PEDIGREE' %meta_typeid_pedigree '=<' meta_pedigree '>' ) $err(meta_pedigree_err) |
('pedigreeDB' %meta_typeid_pedigreedb '=<' meta_pedigreeDB '>' ) $err(meta_pedigreedb_err) |
(meta_typeid '='
(
('<' meta_field (',' meta_field)* '>') |
('"' meta_field_desc '"') |
('<"' meta_field_desc '">') |
meta_value
)
)
) %meta_entry_end;
# Header between meta and records
sample_name = (print - (NL | CS))+ >token_begin @token_middle %sample_name_end;
header = ('#CHROM' CS 'POS' CS 'ID' CS 'REF' CS 'ALT' CS 'QUAL' CS 'FILTER' CS 'INFO' )
$eof(no_newline_at_eof_error) $err(header_prefix_err)
(CS 'FORMAT' (CS sample_name)+ )? $eof(no_newline_at_eof_error) %header_end ;
# Records
position = nat_number ;
record_chrom = chrom_basic >token_begin $token_middle %token_end |
'<' chrom_basic >token_begin $token_middle %token_end '>' ;
record_position = position >token_begin @token_middle %token_end ;
## ID must be a (list of) string with no white-spaces or semi-colons
record_id = (record_id_value (';' record_id_value)*) | record_empty_field ;
record_ref = bases >token_begin @token_middle %token_end ;
## Structural variants follow forms like:
## ]1:1234]ATG or ]<contig_1>:1234]ATG : paired breakends
## .AGT, AGT.: single breakends
record_alt_sv = ']' chromosome ':' position ']' bases |
'[' chromosome ':' position '[' bases |
bases ']' chromosome ':' position ']' |
bases '[' chromosome ':' position '[' |
'.' bases |
bases '.' ;
## Unspecified alleles and REF-only blocks (gVCF)
record_alt_gvcf = '<*>' ;
## Main alternate allele rule
record_alt_data = ( record_alt_snv |
record_alt_indel |
record_alt_sv |
record_alt_gvcf |
record_alt_other ) >token_begin $token_middle %token_end ;
record_alt = (record_alt_data (',' record_alt_data)*) | record_empty_field ;
record_qual = (any_number | '.') >token_begin $token_middle %token_end ;
record_filter = (record_fil_value (';' record_fil_value)*) | record_empty_field ;
info_key = (( (alpha | '_') (alpha | digit | '_' | '.')*) | '1000G' ) ;
info_value = (print - ';')+ ;
info_value_list = info_value (',' info_value)* ;
info_entry = (
info_key $err(info_key_error) '=' info_value_list $err(info_value_error) |
info_key $err(info_key_error)
) >token_begin $token_middle %token_end ;
record_info = ( info_entry (';' info_entry)* ) |
( '.' >token_begin @token_middle %token_end ) ;
## Accepting non-alphanumeric characters is an addition in v4.3, but widely used in already existing files
format_value = ( (alpha | '_') (alnum | '_' | '.' | '%')* ) >token_begin $token_middle %token_end ;
record_format = format_value (':' format_value)* ;
## In a sample, if a genotype is present it must be the first field
record_sample = (
genotype $eof(no_newline_at_eof_error) $err(genotype_error) (':' sample_values)? |
sample_values
) >token_begin $token_middle %token_end ;
record = (
record_chrom %record_field_end $err(chrom_error)
CS record_position %record_field_end $err(pos_error)
CS record_id %record_field_end $err(id_error)
CS record_ref %record_field_end $err(ref_error)
CS record_alt %record_field_end $err(alt_error)
CS record_qual %record_field_end $err(qual_error)
CS record_filter %record_field_end $err(filter_error)
CS record_info %record_field_end $eof(no_newline_at_eof_error) $err(info_error)
(CS record_format %record_field_end $err(format_error)
(CS record_sample %record_field_end $eof(no_newline_at_eof_error) $err(sample_error))+ )?
) %record_end;
fileformat_section = (fileformat NL) $err(fileformat_section_error);
meta_section = (meta_entry NL)* $err(meta_section_error);
header_section = (header NL) $err(header_section_error);
body_section = (record (NL record)*)? $err(body_section_error);
# Machine start (fileformat, then optional meta, header, then optional records)
main := fileformat_section
meta_section
header_section
body_section >meta_section_end
(NL)* ;
# Error recovery machines that skip until the next line and restart the
# the most appropriate section state.
meta_section_skip := [^\n]* NL @{ fgoto meta_section; };
body_section_skip := [^\n]* NL @{ fgoto body_section; };
}%%
namespace
{
%%{
write data;
}%%
}
namespace ebi
{
namespace vcf
{
template <typename Configuration>
ParserImpl_v43<Configuration>::ParserImpl_v43(std::shared_ptr<Source> source, AdditionalChecks additionalChecks)
: ParserImpl{source, additionalChecks}
{
%%{
write init;
}%%
}
template <typename Configuration>
void ParserImpl_v43<Configuration>::parse_buffer(char const * p, char const * pe, char const * eof)
{
%%{
write exec;
}%%
}
}
}