From 3a95d0087b0cb1c9c06255194db4d713486dde1f Mon Sep 17 00:00:00 2001 From: Cristina Yenyxe Gonzalez Garcia Date: Wed, 7 Jan 2015 15:27:20 +0000 Subject: [PATCH] Generic error messages for pedigreeDB and assembly metadata entries. #18 --- cpp/src/bioformats/vcf/vcf_v41.ragel | 16 +- .../bioformats/vcf/vcf_validator_detail.hpp | 1966 +++++++++-------- 2 files changed, 1093 insertions(+), 889 deletions(-) diff --git a/cpp/src/bioformats/vcf/vcf_v41.ragel b/cpp/src/bioformats/vcf/vcf_v41.ragel index b92e022..bfe55b7 100644 --- a/cpp/src/bioformats/vcf/vcf_v41.ragel +++ b/cpp/src/bioformats/vcf/vcf_v41.ragel @@ -230,6 +230,12 @@ fhold; fgoto meta_section_skip; } + # assembly metadata + action meta_assembly_err { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + fhold; fgoto meta_section_skip; + } + # contig metadata action meta_contig_err { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); @@ -290,6 +296,12 @@ fhold; fgoto meta_section_skip; } + # pedigreeDB metadata + action meta_pedigreedb_err { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + fhold; fgoto meta_section_skip; + } + # SAMPLE metadata action meta_sample_err { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); @@ -447,11 +459,11 @@ ("##FILTER=<" meta_filter ">" ) %(meta_filter_read) $err(meta_filter_err) | ("##FORMAT=<" meta_format ">" ) %(meta_format_read) $err(meta_format_err) | ("##INFO=<" meta_info ">" ) %(meta_info_read) $err(meta_info_err) | - ("##assembly=" meta_assembly ) | + ("##assembly=" meta_assembly ) $err(meta_assembly_err) | ("##contig=<" meta_contig ">" ) $err(meta_contig_err) | ("##SAMPLE=<" meta_sample ">" ) $err(meta_sample_err) | ("##PEDIGREE=<" meta_pedigree ">" ) $err(meta_pedigree_err) | - ("##pedigreeDB=<" meta_pedigreeDB ">" ) | + ("##pedigreeDB=<" meta_pedigreeDB ">" ) $err(meta_pedigreedb_err) | ("##" meta_field >token_begin %meta_field_value_end) | ("##" meta_field_value >token_begin %meta_field_value_end) ) diff --git a/cpp/src/bioformats/vcf/vcf_validator_detail.hpp b/cpp/src/bioformats/vcf/vcf_validator_detail.hpp index 2a8b85b..9cf36ba 100644 --- a/cpp/src/bioformats/vcf/vcf_validator_detail.hpp +++ b/cpp/src/bioformats/vcf/vcf_validator_detail.hpp @@ -5,7 +5,7 @@ #include "vcf_validator.hpp" -#line 567 "vcf_v41.ragel" +#line 579 "vcf_v41.ragel" namespace @@ -23,7 +23,7 @@ static const int vcf_en_meta_section_skip = 702; static const int vcf_en_body_section_skip = 703; -#line 573 "vcf_v41.ragel" +#line 585 "vcf_v41.ragel" } @@ -40,7 +40,7 @@ namespace opencb cs = vcf_start; } -#line 585 "vcf_v41.ragel" +#line 597 "vcf_v41.ragel" } @@ -77,7 +77,7 @@ namespace opencb return cs >= #line 79 "vcf_validator_detail.hpp" 704 -#line 618 "vcf_v41.ragel" +#line 630 "vcf_v41.ragel" ; } @@ -124,7 +124,7 @@ case 1: ErrorPolicy::handle_fileformat_section_error(*this); p--; {goto st702;} } -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -134,36 +134,46 @@ case 1: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -176,7 +186,7 @@ case 1: } goto st0; tr20: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -186,36 +196,46 @@ case 1: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -228,7 +248,7 @@ case 1: } goto st0; tr23: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -238,36 +258,46 @@ case 1: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -282,7 +312,7 @@ case 1: } goto st0; tr37: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -294,7 +324,7 @@ case 1: } goto st0; tr142: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -362,7 +392,7 @@ case 1: } goto st0; tr174: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} @@ -396,17 +426,17 @@ case 1: } goto st0; tr195: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -418,12 +448,12 @@ case 1: } goto st0; tr198: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -435,7 +465,7 @@ case 1: } goto st0; tr204: -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -447,12 +477,12 @@ case 1: } goto st0; tr209: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -464,12 +494,12 @@ case 1: } goto st0; tr229: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -481,12 +511,12 @@ case 1: } goto st0; tr233: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -498,7 +528,7 @@ case 1: } goto st0; tr239: -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -510,12 +540,12 @@ case 1: } goto st0; tr244: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -527,12 +557,12 @@ case 1: } goto st0; tr257: -#line 251 "vcf_v41.ragel" +#line 257 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "FORMAT metadata Number is not a number, A, R, G or dot"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -544,12 +574,12 @@ case 1: } goto st0; tr266: -#line 256 "vcf_v41.ragel" +#line 262 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "FORMAT metadata Type is not a Integer, Float, Character or String"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -561,12 +591,12 @@ case 1: } goto st0; tr294: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -578,12 +608,12 @@ case 1: } goto st0; tr308: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -595,7 +625,7 @@ case 1: } goto st0; tr313: -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -607,12 +637,12 @@ case 1: } goto st0; tr318: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -624,12 +654,12 @@ case 1: } goto st0; tr331: -#line 267 "vcf_v41.ragel" +#line 273 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Number is not a number, A, R, G or dot"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -641,12 +671,12 @@ case 1: } goto st0; tr340: -#line 272 "vcf_v41.ragel" +#line 278 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Type is not a Integer, Float, Flag, Character or String"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -658,12 +688,12 @@ case 1: } goto st0; tr368: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -675,22 +705,22 @@ case 1: } goto st0; tr370: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -702,17 +732,17 @@ case 1: } goto st0; tr373: -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -724,12 +754,12 @@ case 1: } goto st0; tr376: -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -741,12 +771,12 @@ case 1: } goto st0; tr387: -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -758,12 +788,12 @@ case 1: } goto st0; tr409: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} @@ -775,7 +805,7 @@ case 1: } goto st0; tr418: -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} @@ -787,12 +817,12 @@ case 1: } goto st0; tr420: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} @@ -804,12 +834,12 @@ case 1: } goto st0; tr432: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -821,7 +851,7 @@ case 1: } goto st0; tr439: -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -833,12 +863,12 @@ case 1: } goto st0; tr444: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -850,17 +880,17 @@ case 1: } goto st0; tr449: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -872,12 +902,12 @@ case 1: } goto st0; tr451: -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -889,17 +919,17 @@ case 1: } goto st0; tr464: -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -911,12 +941,12 @@ case 1: } goto st0; tr466: -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -928,17 +958,17 @@ case 1: } goto st0; tr479: -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -950,12 +980,12 @@ case 1: } goto st0; tr481: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -966,25 +996,47 @@ case 1: p--; {goto st702;} } goto st0; -tr506: -#line 325 "vcf_v41.ragel" +tr498: +#line 322 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); + p--; {goto st702;} + } +#line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + goto st0; +tr507: +#line 337 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); p--; {goto st702;} } +#line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); p--; {goto st702;} } goto st0; -tr513: -#line 310 "vcf_v41.ragel" +tr514: +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -995,8 +1047,8 @@ case 1: p--; {goto st702;} } goto st0; -tr520: -#line 234 "vcf_v41.ragel" +tr521: +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -1007,13 +1059,13 @@ case 1: p--; {goto st702;} } goto st0; -tr525: -#line 315 "vcf_v41.ragel" +tr526: +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -1024,13 +1076,13 @@ case 1: p--; {goto st702;} } goto st0; -tr535: -#line 325 "vcf_v41.ragel" +tr536: +#line 337 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -1041,15 +1093,61 @@ case 1: p--; {goto st702;} } goto st0; -tr561: +tr544: +#line 322 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); + p--; {goto st702;} + } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + goto st0; +tr555: +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + goto st0; +tr557: +#line 337 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); + p--; {goto st702;} + } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + goto st0; +tr565: #line 45 "vcf_v41.ragel" { ErrorPolicy::handle_header_section_error(*this); p--; {goto st703;} } goto st0; -tr611: -#line 332 "vcf_v41.ragel" +tr615: +#line 344 "vcf_v41.ragel" { printf("Line %zu: Error in 'chrom' field\n", n_lines); p--; {goto st703;} @@ -1060,8 +1158,8 @@ case 1: p--; {goto st703;} } goto st0; -tr614: -#line 337 "vcf_v41.ragel" +tr618: +#line 349 "vcf_v41.ragel" { ErrorPolicy::handle_body_section_error(*this, "Position is not a positive number"); p--; {goto st703;} @@ -1072,8 +1170,8 @@ case 1: p--; {goto st703;} } goto st0; -tr618: -#line 342 "vcf_v41.ragel" +tr622: +#line 354 "vcf_v41.ragel" { printf("Line %zu: Error in 'id' field\n", n_lines); p--; {goto st703;} @@ -1084,8 +1182,8 @@ case 1: p--; {goto st703;} } goto st0; -tr623: -#line 347 "vcf_v41.ragel" +tr627: +#line 359 "vcf_v41.ragel" { printf("Line %zu: Error in 'reference' field\n", n_lines); p--; {goto st703;} @@ -1096,8 +1194,8 @@ case 1: p--; {goto st703;} } goto st0; -tr627: -#line 352 "vcf_v41.ragel" +tr631: +#line 364 "vcf_v41.ragel" { printf("Line %zu: Error in 'alternate' field\n", n_lines); p--; {goto st703;} @@ -1108,8 +1206,8 @@ case 1: p--; {goto st703;} } goto st0; -tr636: -#line 357 "vcf_v41.ragel" +tr640: +#line 369 "vcf_v41.ragel" { printf("Line %zu: Error in 'quality' field\n", n_lines); p--; {goto st703;} @@ -1120,8 +1218,8 @@ case 1: p--; {goto st703;} } goto st0; -tr640: -#line 362 "vcf_v41.ragel" +tr644: +#line 374 "vcf_v41.ragel" { printf("Line %zu: Error in 'filter' field\n", n_lines); p--; {goto st703;} @@ -1132,8 +1230,8 @@ case 1: p--; {goto st703;} } goto st0; -tr645: -#line 367 "vcf_v41.ragel" +tr649: +#line 379 "vcf_v41.ragel" { printf("Line %zu: Error in 'info' field\n", n_lines); p--; {goto st703;} @@ -1144,8 +1242,8 @@ case 1: p--; {goto st703;} } goto st0; -tr663: -#line 372 "vcf_v41.ragel" +tr667: +#line 384 "vcf_v41.ragel" { printf("Line %zu: Error in 'format' field\n", n_lines); p--; {goto st703;} @@ -1156,8 +1254,8 @@ case 1: p--; {goto st703;} } goto st0; -tr672: -#line 377 "vcf_v41.ragel" +tr676: +#line 389 "vcf_v41.ragel" { ErrorPolicy::handle_body_section_error(*this, "Incorrect sample format"); p--; {goto st703;} @@ -1168,13 +1266,13 @@ case 1: p--; {goto st703;} } goto st0; -tr811: +tr815: #line 45 "vcf_v41.ragel" { ErrorPolicy::handle_header_section_error(*this); p--; {goto st703;} } -#line 332 "vcf_v41.ragel" +#line 344 "vcf_v41.ragel" { printf("Line %zu: Error in 'chrom' field\n", n_lines); p--; {goto st703;} @@ -1185,7 +1283,7 @@ case 1: p--; {goto st703;} } goto st0; -#line 1189 "vcf_validator_detail.hpp" +#line 1287 "vcf_validator_detail.hpp" st0: cs = 0; goto _out; @@ -1290,7 +1388,7 @@ case 14: if ( ++p == pe ) goto _test_eof15; case 15: -#line 1294 "vcf_validator_detail.hpp" +#line 1392 "vcf_validator_detail.hpp" if ( (*p) == 10 ) goto tr16; if ( 33 <= (*p) && (*p) <= 126 ) @@ -1311,7 +1409,7 @@ case 15: if ( ++p == pe ) goto _test_eof16; case 16: -#line 1315 "vcf_validator_detail.hpp" +#line 1413 "vcf_validator_detail.hpp" if ( (*p) == 35 ) goto tr19; goto tr18; @@ -1326,7 +1424,7 @@ case 16: if ( ++p == pe ) goto _test_eof17; case 17: -#line 1330 "vcf_validator_detail.hpp" +#line 1428 "vcf_validator_detail.hpp" switch( (*p) ) { case 35: goto st18; case 67: goto st500; @@ -1381,7 +1479,7 @@ case 18: if ( ++p == pe ) goto _test_eof19; case 19: -#line 1385 "vcf_validator_detail.hpp" +#line 1483 "vcf_validator_detail.hpp" if ( (*p) == 10 ) goto tr35; if ( (*p) > 60 ) { @@ -1501,7 +1599,7 @@ case 19: if ( ++p == pe ) goto _test_eof20; case 20: -#line 1505 "vcf_validator_detail.hpp" +#line 1603 "vcf_validator_detail.hpp" if ( (*p) == 35 ) goto tr19; goto tr20; @@ -1515,7 +1613,7 @@ case 20: if ( ++p == pe ) goto _test_eof21; case 21: -#line 1519 "vcf_validator_detail.hpp" +#line 1617 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -1552,7 +1650,7 @@ case 21: if ( ++p == pe ) goto _test_eof22; case 22: -#line 1556 "vcf_validator_detail.hpp" +#line 1654 "vcf_validator_detail.hpp" if ( (*p) == 60 ) goto st23; if ( (*p) > 59 ) { @@ -1611,7 +1709,7 @@ case 23: if ( ++p == pe ) goto _test_eof24; case 24: -#line 1615 "vcf_validator_detail.hpp" +#line 1713 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -1678,7 +1776,7 @@ case 26: if ( ++p == pe ) goto _test_eof27; case 27: -#line 1682 "vcf_validator_detail.hpp" +#line 1780 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 62: goto tr54; @@ -1726,7 +1824,7 @@ case 27: if ( ++p == pe ) goto _test_eof28; case 28: -#line 1730 "vcf_validator_detail.hpp" +#line 1828 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -1770,7 +1868,7 @@ case 28: if ( ++p == pe ) goto _test_eof29; case 29: -#line 1774 "vcf_validator_detail.hpp" +#line 1872 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr65; case 44: goto tr53; @@ -1792,7 +1890,7 @@ case 29: if ( ++p == pe ) goto _test_eof30; case 30: -#line 1796 "vcf_validator_detail.hpp" +#line 1894 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -1896,7 +1994,7 @@ case 32: if ( ++p == pe ) goto _test_eof33; case 33: -#line 1900 "vcf_validator_detail.hpp" +#line 1998 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -2160,7 +2258,7 @@ case 40: if ( ++p == pe ) goto _test_eof41; case 41: -#line 2164 "vcf_validator_detail.hpp" +#line 2262 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -2263,7 +2361,7 @@ case 43: if ( ++p == pe ) goto _test_eof44; case 44: -#line 2267 "vcf_validator_detail.hpp" +#line 2365 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -2494,7 +2592,7 @@ case 50: if ( ++p == pe ) goto _test_eof51; case 51: -#line 2498 "vcf_validator_detail.hpp" +#line 2596 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -2629,7 +2727,7 @@ case 54: if ( ++p == pe ) goto _test_eof55; case 55: -#line 2633 "vcf_validator_detail.hpp" +#line 2731 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -2860,7 +2958,7 @@ case 61: if ( ++p == pe ) goto _test_eof62; case 62: -#line 2864 "vcf_validator_detail.hpp" +#line 2962 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -3027,7 +3125,7 @@ case 66: if ( ++p == pe ) goto _test_eof67; case 67: -#line 3031 "vcf_validator_detail.hpp" +#line 3129 "vcf_validator_detail.hpp" switch( (*p) ) { case 44: goto tr53; case 61: goto st25; @@ -3322,7 +3420,7 @@ case 75: if ( ++p == pe ) goto _test_eof76; case 76: -#line 3326 "vcf_validator_detail.hpp" +#line 3424 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -3423,7 +3521,7 @@ case 78: if ( ++p == pe ) goto _test_eof79; case 79: -#line 3427 "vcf_validator_detail.hpp" +#line 3525 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -3679,7 +3777,7 @@ case 86: if ( ++p == pe ) goto _test_eof87; case 87: -#line 3683 "vcf_validator_detail.hpp" +#line 3781 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -3779,7 +3877,7 @@ case 89: if ( ++p == pe ) goto _test_eof90; case 90: -#line 3783 "vcf_validator_detail.hpp" +#line 3881 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -4003,7 +4101,7 @@ case 96: if ( ++p == pe ) goto _test_eof97; case 97: -#line 4007 "vcf_validator_detail.hpp" +#line 4105 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -4134,7 +4232,7 @@ case 100: if ( ++p == pe ) goto _test_eof101; case 101: -#line 4138 "vcf_validator_detail.hpp" +#line 4236 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -4358,7 +4456,7 @@ case 107: if ( ++p == pe ) goto _test_eof108; case 108: -#line 4362 "vcf_validator_detail.hpp" +#line 4460 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -4520,7 +4618,7 @@ case 112: if ( ++p == pe ) goto _test_eof113; case 113: -#line 4524 "vcf_validator_detail.hpp" +#line 4622 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto st25; @@ -4806,7 +4904,7 @@ case 121: if ( ++p == pe ) goto _test_eof122; case 122: -#line 4810 "vcf_validator_detail.hpp" +#line 4908 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -5316,7 +5414,7 @@ case 168: if ( ++p == pe ) goto _test_eof169; case 169: -#line 5320 "vcf_validator_detail.hpp" +#line 5418 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -6429,7 +6527,7 @@ case 269: if ( ++p == pe ) goto _test_eof270; case 270: -#line 6433 "vcf_validator_detail.hpp" +#line 6531 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -7260,7 +7358,7 @@ case 360: if ( ++p == pe ) goto _test_eof361; case 361: -#line 7264 "vcf_validator_detail.hpp" +#line 7362 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -7713,7 +7811,7 @@ case 380: if ( ++p == pe ) goto _test_eof381; case 381: -#line 7717 "vcf_validator_detail.hpp" +#line 7815 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -8447,7 +8545,7 @@ case 438: if ( ++p == pe ) goto _test_eof439; case 439: -#line 8451 "vcf_validator_detail.hpp" +#line 8549 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -8474,7 +8572,7 @@ case 439: goto st21; } else goto st21; - goto tr37; + goto tr498; st440: if ( ++p == pe ) goto _test_eof440; @@ -8505,7 +8603,7 @@ case 440: goto st21; } else goto st21; - goto tr37; + goto tr498; st441: if ( ++p == pe ) goto _test_eof441; @@ -8536,7 +8634,7 @@ case 441: goto st21; } else goto st21; - goto tr37; + goto tr498; st442: if ( ++p == pe ) goto _test_eof442; @@ -8567,7 +8665,7 @@ case 442: goto st21; } else goto st21; - goto tr37; + goto tr498; st443: if ( ++p == pe ) goto _test_eof443; @@ -8598,7 +8696,7 @@ case 443: goto st21; } else goto st21; - goto tr37; + goto tr498; st444: if ( ++p == pe ) goto _test_eof444; @@ -8629,7 +8727,7 @@ case 444: goto st21; } else goto st21; - goto tr37; + goto tr498; st445: if ( ++p == pe ) goto _test_eof445; @@ -8660,7 +8758,7 @@ case 445: goto st21; } else goto st21; - goto tr37; + goto tr498; st446: if ( ++p == pe ) goto _test_eof446; @@ -8690,7 +8788,7 @@ case 446: goto st21; } else goto st21; - goto tr37; + goto tr498; st447: if ( ++p == pe ) goto _test_eof447; @@ -8700,17 +8798,17 @@ case 447: goto st448; } else if ( (*p) >= 65 ) goto st448; - goto tr506; + goto tr507; st448: if ( ++p == pe ) goto _test_eof448; case 448: switch( (*p) ) { - case 10: goto tr506; - case 35: goto tr506; - case 47: goto tr506; - case 58: goto tr506; - case 63: goto tr506; + case 10: goto tr507; + case 35: goto tr507; + case 47: goto tr507; + case 58: goto tr507; + case 63: goto tr507; } goto st449; st449: @@ -8718,11 +8816,11 @@ case 448: goto _test_eof449; case 449: switch( (*p) ) { - case 10: goto tr506; - case 35: goto tr506; - case 47: goto tr506; + case 10: goto tr507; + case 35: goto tr507; + case 47: goto tr507; case 58: goto st450; - case 63: goto tr506; + case 63: goto tr507; } goto st449; st450: @@ -8731,14 +8829,14 @@ case 449: case 450: if ( (*p) == 47 ) goto st451; - goto tr506; + goto tr507; st451: if ( ++p == pe ) goto _test_eof451; case 451: if ( (*p) == 47 ) goto st452; - goto tr506; + goto tr507; st452: if ( ++p == pe ) goto _test_eof452; @@ -8748,7 +8846,7 @@ case 452: goto st453; } else if ( (*p) >= 65 ) goto st453; - goto tr506; + goto tr507; st453: if ( ++p == pe ) goto _test_eof453; @@ -8766,7 +8864,7 @@ case 453: if ( ++p == pe ) goto _test_eof454; case 454: -#line 8770 "vcf_validator_detail.hpp" +#line 8868 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -8793,7 +8891,7 @@ case 454: goto st21; } else goto st21; - goto tr513; + goto tr514; st455: if ( ++p == pe ) goto _test_eof455; @@ -8824,7 +8922,7 @@ case 455: goto st21; } else goto st21; - goto tr513; + goto tr514; st456: if ( ++p == pe ) goto _test_eof456; @@ -8855,7 +8953,7 @@ case 456: goto st21; } else goto st21; - goto tr513; + goto tr514; st457: if ( ++p == pe ) goto _test_eof457; @@ -8886,7 +8984,7 @@ case 457: goto st21; } else goto st21; - goto tr513; + goto tr514; st458: if ( ++p == pe ) goto _test_eof458; @@ -8917,7 +9015,7 @@ case 458: goto st21; } else goto st21; - goto tr513; + goto tr514; st459: if ( ++p == pe ) goto _test_eof459; @@ -8947,35 +9045,35 @@ case 459: goto st21; } else goto st21; - goto tr513; + goto tr514; st460: if ( ++p == pe ) goto _test_eof460; case 460: if ( (*p) == 60 ) goto st461; - goto tr520; + goto tr521; st461: if ( ++p == pe ) goto _test_eof461; case 461: if ( (*p) == 73 ) goto st462; - goto tr520; + goto tr521; st462: if ( ++p == pe ) goto _test_eof462; case 462: if ( (*p) == 68 ) goto st463; - goto tr520; + goto tr521; st463: if ( ++p == pe ) goto _test_eof463; case 463: if ( (*p) == 61 ) goto st464; - goto tr520; + goto tr521; st464: if ( ++p == pe ) goto _test_eof464; @@ -8993,7 +9091,7 @@ case 464: goto st466; } else goto st466; - goto tr525; + goto tr526; st465: if ( ++p == pe ) goto _test_eof465; @@ -9011,7 +9109,7 @@ case 465: goto st466; } else goto st466; - goto tr525; + goto tr526; st466: if ( ++p == pe ) goto _test_eof466; @@ -9031,35 +9129,35 @@ case 466: goto st466; } else goto st466; - goto tr525; + goto tr526; st467: if ( ++p == pe ) goto _test_eof467; case 467: if ( (*p) == 85 ) goto st468; - goto tr520; + goto tr521; st468: if ( ++p == pe ) goto _test_eof468; case 468: if ( (*p) == 82 ) goto st469; - goto tr520; + goto tr521; st469: if ( ++p == pe ) goto _test_eof469; case 469: if ( (*p) == 76 ) goto st470; - goto tr520; + goto tr521; st470: if ( ++p == pe ) goto _test_eof470; case 470: if ( (*p) == 61 ) goto st471; - goto tr520; + goto tr521; st471: if ( ++p == pe ) goto _test_eof471; @@ -9069,17 +9167,17 @@ case 471: goto st472; } else if ( (*p) >= 65 ) goto st472; - goto tr535; + goto tr536; st472: if ( ++p == pe ) goto _test_eof472; case 472: switch( (*p) ) { - case 10: goto tr535; - case 35: goto tr535; - case 47: goto tr535; - case 58: goto tr535; - case 63: goto tr535; + case 10: goto tr536; + case 35: goto tr536; + case 47: goto tr536; + case 58: goto tr536; + case 63: goto tr536; } goto st473; st473: @@ -9087,11 +9185,11 @@ case 472: goto _test_eof473; case 473: switch( (*p) ) { - case 10: goto tr535; - case 35: goto tr535; - case 47: goto tr535; + case 10: goto tr536; + case 35: goto tr536; + case 47: goto tr536; case 58: goto st474; - case 63: goto tr535; + case 63: goto tr536; } goto st473; st474: @@ -9100,14 +9198,14 @@ case 473: case 474: if ( (*p) == 47 ) goto st475; - goto tr535; + goto tr536; st475: if ( ++p == pe ) goto _test_eof475; case 475: if ( (*p) == 47 ) goto st476; - goto tr535; + goto tr536; st476: if ( ++p == pe ) goto _test_eof476; @@ -9117,13 +9215,13 @@ case 476: goto st477; } else if ( (*p) >= 65 ) goto st477; - goto tr535; + goto tr536; st477: if ( ++p == pe ) goto _test_eof477; case 477: switch( (*p) ) { - case 10: goto tr535; + case 10: goto tr536; case 62: goto st478; } goto st477; @@ -9153,7 +9251,7 @@ case 479: goto st466; } else goto st466; - goto tr525; + goto tr526; st480: if ( ++p == pe ) goto _test_eof480; @@ -9171,7 +9269,7 @@ case 480: goto st466; } else goto st466; - goto tr525; + goto tr526; tr33: #line 15 "vcf_v41.ragel" { @@ -9182,7 +9280,7 @@ case 480: if ( ++p == pe ) goto _test_eof481; case 481: -#line 9186 "vcf_validator_detail.hpp" +#line 9284 "vcf_validator_detail.hpp" switch( (*p) ) { case 10: goto tr35; case 61: goto tr39; @@ -9209,7 +9307,7 @@ case 481: goto st21; } else goto st21; - goto tr37; + goto tr544; st482: if ( ++p == pe ) goto _test_eof482; @@ -9240,7 +9338,7 @@ case 482: goto st21; } else goto st21; - goto tr37; + goto tr544; st483: if ( ++p == pe ) goto _test_eof483; @@ -9271,7 +9369,7 @@ case 483: goto st21; } else goto st21; - goto tr37; + goto tr544; st484: if ( ++p == pe ) goto _test_eof484; @@ -9302,7 +9400,7 @@ case 484: goto st21; } else goto st21; - goto tr37; + goto tr544; st485: if ( ++p == pe ) goto _test_eof485; @@ -9333,7 +9431,7 @@ case 485: goto st21; } else goto st21; - goto tr37; + goto tr544; st486: if ( ++p == pe ) goto _test_eof486; @@ -9364,7 +9462,7 @@ case 486: goto st21; } else goto st21; - goto tr37; + goto tr544; st487: if ( ++p == pe ) goto _test_eof487; @@ -9395,7 +9493,7 @@ case 487: goto st21; } else goto st21; - goto tr37; + goto tr544; st488: if ( ++p == pe ) goto _test_eof488; @@ -9426,7 +9524,7 @@ case 488: goto st21; } else goto st21; - goto tr37; + goto tr544; st489: if ( ++p == pe ) goto _test_eof489; @@ -9457,7 +9555,7 @@ case 489: goto st21; } else goto st21; - goto tr37; + goto tr544; st490: if ( ++p == pe ) goto _test_eof490; @@ -9487,14 +9585,14 @@ case 490: goto st21; } else goto st21; - goto tr37; + goto tr544; st491: if ( ++p == pe ) goto _test_eof491; case 491: if ( (*p) == 60 ) goto st492; - goto tr34; + goto tr555; st492: if ( ++p == pe ) goto _test_eof492; @@ -9504,17 +9602,17 @@ case 492: goto st493; } else if ( (*p) >= 65 ) goto st493; - goto tr506; + goto tr557; st493: if ( ++p == pe ) goto _test_eof493; case 493: switch( (*p) ) { - case 10: goto tr506; - case 35: goto tr506; - case 47: goto tr506; - case 58: goto tr506; - case 63: goto tr506; + case 10: goto tr557; + case 35: goto tr557; + case 47: goto tr557; + case 58: goto tr557; + case 63: goto tr557; } goto st494; st494: @@ -9522,11 +9620,11 @@ case 493: goto _test_eof494; case 494: switch( (*p) ) { - case 10: goto tr506; - case 35: goto tr506; - case 47: goto tr506; + case 10: goto tr557; + case 35: goto tr557; + case 47: goto tr557; case 58: goto st495; - case 63: goto tr506; + case 63: goto tr557; } goto st494; st495: @@ -9535,14 +9633,14 @@ case 494: case 495: if ( (*p) == 47 ) goto st496; - goto tr506; + goto tr557; st496: if ( ++p == pe ) goto _test_eof496; case 496: if ( (*p) == 47 ) goto st497; - goto tr506; + goto tr557; st497: if ( ++p == pe ) goto _test_eof497; @@ -9552,13 +9650,13 @@ case 497: goto st498; } else if ( (*p) >= 65 ) goto st498; - goto tr506; + goto tr557; st498: if ( ++p == pe ) goto _test_eof498; case 498: switch( (*p) ) { - case 10: goto tr506; + case 10: goto tr557; case 62: goto st499; } goto st498; @@ -9577,311 +9675,311 @@ case 499: case 500: if ( (*p) == 72 ) goto st501; - goto tr561; + goto tr565; st501: if ( ++p == pe ) goto _test_eof501; case 501: if ( (*p) == 82 ) goto st502; - goto tr561; + goto tr565; st502: if ( ++p == pe ) goto _test_eof502; case 502: if ( (*p) == 79 ) goto st503; - goto tr561; + goto tr565; st503: if ( ++p == pe ) goto _test_eof503; case 503: if ( (*p) == 77 ) goto st504; - goto tr561; + goto tr565; st504: if ( ++p == pe ) goto _test_eof504; case 504: if ( (*p) == 9 ) goto st505; - goto tr561; + goto tr565; st505: if ( ++p == pe ) goto _test_eof505; case 505: if ( (*p) == 80 ) goto st506; - goto tr561; + goto tr565; st506: if ( ++p == pe ) goto _test_eof506; case 506: if ( (*p) == 79 ) goto st507; - goto tr561; + goto tr565; st507: if ( ++p == pe ) goto _test_eof507; case 507: if ( (*p) == 83 ) goto st508; - goto tr561; + goto tr565; st508: if ( ++p == pe ) goto _test_eof508; case 508: if ( (*p) == 9 ) goto st509; - goto tr561; + goto tr565; st509: if ( ++p == pe ) goto _test_eof509; case 509: if ( (*p) == 73 ) goto st510; - goto tr561; + goto tr565; st510: if ( ++p == pe ) goto _test_eof510; case 510: if ( (*p) == 68 ) goto st511; - goto tr561; + goto tr565; st511: if ( ++p == pe ) goto _test_eof511; case 511: if ( (*p) == 9 ) goto st512; - goto tr561; + goto tr565; st512: if ( ++p == pe ) goto _test_eof512; case 512: if ( (*p) == 82 ) goto st513; - goto tr561; + goto tr565; st513: if ( ++p == pe ) goto _test_eof513; case 513: if ( (*p) == 69 ) goto st514; - goto tr561; + goto tr565; st514: if ( ++p == pe ) goto _test_eof514; case 514: if ( (*p) == 70 ) goto st515; - goto tr561; + goto tr565; st515: if ( ++p == pe ) goto _test_eof515; case 515: if ( (*p) == 9 ) goto st516; - goto tr561; + goto tr565; st516: if ( ++p == pe ) goto _test_eof516; case 516: if ( (*p) == 65 ) goto st517; - goto tr561; + goto tr565; st517: if ( ++p == pe ) goto _test_eof517; case 517: if ( (*p) == 76 ) goto st518; - goto tr561; + goto tr565; st518: if ( ++p == pe ) goto _test_eof518; case 518: if ( (*p) == 84 ) goto st519; - goto tr561; + goto tr565; st519: if ( ++p == pe ) goto _test_eof519; case 519: if ( (*p) == 9 ) goto st520; - goto tr561; + goto tr565; st520: if ( ++p == pe ) goto _test_eof520; case 520: if ( (*p) == 81 ) goto st521; - goto tr561; + goto tr565; st521: if ( ++p == pe ) goto _test_eof521; case 521: if ( (*p) == 85 ) goto st522; - goto tr561; + goto tr565; st522: if ( ++p == pe ) goto _test_eof522; case 522: if ( (*p) == 65 ) goto st523; - goto tr561; + goto tr565; st523: if ( ++p == pe ) goto _test_eof523; case 523: if ( (*p) == 76 ) goto st524; - goto tr561; + goto tr565; st524: if ( ++p == pe ) goto _test_eof524; case 524: if ( (*p) == 9 ) goto st525; - goto tr561; + goto tr565; st525: if ( ++p == pe ) goto _test_eof525; case 525: if ( (*p) == 70 ) goto st526; - goto tr561; + goto tr565; st526: if ( ++p == pe ) goto _test_eof526; case 526: if ( (*p) == 73 ) goto st527; - goto tr561; + goto tr565; st527: if ( ++p == pe ) goto _test_eof527; case 527: if ( (*p) == 76 ) goto st528; - goto tr561; + goto tr565; st528: if ( ++p == pe ) goto _test_eof528; case 528: if ( (*p) == 84 ) goto st529; - goto tr561; + goto tr565; st529: if ( ++p == pe ) goto _test_eof529; case 529: if ( (*p) == 69 ) goto st530; - goto tr561; + goto tr565; st530: if ( ++p == pe ) goto _test_eof530; case 530: if ( (*p) == 82 ) goto st531; - goto tr561; + goto tr565; st531: if ( ++p == pe ) goto _test_eof531; case 531: if ( (*p) == 9 ) goto st532; - goto tr561; + goto tr565; st532: if ( ++p == pe ) goto _test_eof532; case 532: if ( (*p) == 73 ) goto st533; - goto tr561; + goto tr565; st533: if ( ++p == pe ) goto _test_eof533; case 533: if ( (*p) == 78 ) goto st534; - goto tr561; + goto tr565; st534: if ( ++p == pe ) goto _test_eof534; case 534: if ( (*p) == 70 ) goto st535; - goto tr561; + goto tr565; st535: if ( ++p == pe ) goto _test_eof535; case 535: if ( (*p) == 79 ) goto st536; - goto tr561; + goto tr565; st536: if ( ++p == pe ) goto _test_eof536; case 536: switch( (*p) ) { case 9: goto st537; - case 10: goto tr599; + case 10: goto tr603; } - goto tr561; + goto tr565; st537: if ( ++p == pe ) goto _test_eof537; case 537: if ( (*p) == 70 ) goto st538; - goto tr561; + goto tr565; st538: if ( ++p == pe ) goto _test_eof538; case 538: if ( (*p) == 79 ) goto st539; - goto tr561; + goto tr565; st539: if ( ++p == pe ) goto _test_eof539; case 539: if ( (*p) == 82 ) goto st540; - goto tr561; + goto tr565; st540: if ( ++p == pe ) goto _test_eof540; case 540: if ( (*p) == 77 ) goto st541; - goto tr561; + goto tr565; st541: if ( ++p == pe ) goto _test_eof541; case 541: if ( (*p) == 65 ) goto st542; - goto tr561; + goto tr565; st542: if ( ++p == pe ) goto _test_eof542; case 542: if ( (*p) == 84 ) goto st543; - goto tr561; + goto tr565; st543: if ( ++p == pe ) goto _test_eof543; case 543: if ( (*p) == 9 ) goto st544; - goto tr561; -tr608: + goto tr565; +tr612: #line 110 "vcf_v41.ragel" { // add_vcf_sample_name(ts, p-ts, file); @@ -9891,11 +9989,11 @@ case 543: if ( ++p == pe ) goto _test_eof544; case 544: -#line 9895 "vcf_validator_detail.hpp" +#line 9993 "vcf_validator_detail.hpp" if ( 32 <= (*p) && (*p) <= 126 ) - goto tr607; - goto tr561; -tr607: + goto tr611; + goto tr565; +tr611: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -9905,22 +10003,22 @@ case 544: if ( ++p == pe ) goto _test_eof545; case 545: -#line 9909 "vcf_validator_detail.hpp" +#line 10007 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr608; - case 10: goto tr609; + case 9: goto tr612; + case 10: goto tr613; } if ( 32 <= (*p) && (*p) <= 126 ) goto st545; - goto tr561; -tr599: + goto tr565; +tr603: #line 23 "vcf_v41.ragel" { ++n_lines; n_columns = 1; } goto st704; -tr609: +tr613: #line 110 "vcf_v41.ragel" { // add_vcf_sample_name(ts, p-ts, file); @@ -9935,19 +10033,19 @@ case 545: if ( ++p == pe ) goto _test_eof704; case 704: -#line 9939 "vcf_validator_detail.hpp" +#line 10037 "vcf_validator_detail.hpp" if ( (*p) == 60 ) - goto tr813; + goto tr817; if ( (*p) < 59 ) { if ( 33 <= (*p) && (*p) <= 57 ) - goto tr812; + goto tr816; } else if ( (*p) > 61 ) { if ( 63 <= (*p) && (*p) <= 126 ) - goto tr812; + goto tr816; } else - goto tr812; - goto tr811; -tr812: + goto tr816; + goto tr815; +tr816: #line 114 "vcf_v41.ragel" { // status->current_record = vcf_record_new(); @@ -9962,9 +10060,9 @@ case 704: if ( ++p == pe ) goto _test_eof546; case 546: -#line 9966 "vcf_validator_detail.hpp" +#line 10064 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr612; + case 9: goto tr616; case 59: goto st546; case 61: goto st546; } @@ -9973,8 +10071,8 @@ case 546: goto st546; } else if ( (*p) >= 33 ) goto st546; - goto tr611; -tr612: + goto tr615; +tr616: #line 143 "vcf_v41.ragel" { // set_vcf_record_chromosome(ts, p-ts, status->current_record); @@ -9988,11 +10086,11 @@ case 546: if ( ++p == pe ) goto _test_eof547; case 547: -#line 9992 "vcf_validator_detail.hpp" +#line 10090 "vcf_validator_detail.hpp" if ( 48 <= (*p) && (*p) <= 57 ) - goto tr615; - goto tr614; -tr615: + goto tr619; + goto tr618; +tr619: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10002,13 +10100,13 @@ case 547: if ( ++p == pe ) goto _test_eof548; case 548: -#line 10006 "vcf_validator_detail.hpp" +#line 10104 "vcf_validator_detail.hpp" if ( (*p) == 9 ) - goto tr616; + goto tr620; if ( 48 <= (*p) && (*p) <= 57 ) goto st548; - goto tr614; -tr616: + goto tr618; +tr620: #line 147 "vcf_v41.ragel" { // char *field = strndup(ts, p-ts); @@ -10024,14 +10122,14 @@ case 548: if ( ++p == pe ) goto _test_eof549; case 549: -#line 10028 "vcf_validator_detail.hpp" +#line 10126 "vcf_validator_detail.hpp" if ( (*p) > 58 ) { if ( 60 <= (*p) && (*p) <= 126 ) - goto tr619; + goto tr623; } else if ( (*p) >= 33 ) - goto tr619; - goto tr618; -tr619: + goto tr623; + goto tr622; +tr623: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10041,15 +10139,15 @@ case 549: if ( ++p == pe ) goto _test_eof550; case 550: -#line 10045 "vcf_validator_detail.hpp" +#line 10143 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr620; + case 9: goto tr624; case 59: goto st701; } if ( 33 <= (*p) && (*p) <= 126 ) goto st550; - goto tr618; -tr620: + goto tr622; +tr624: #line 153 "vcf_v41.ragel" { // set_vcf_record_id(ts, p-ts, status->current_record); @@ -10063,21 +10161,21 @@ case 550: if ( ++p == pe ) goto _test_eof551; case 551: -#line 10067 "vcf_validator_detail.hpp" - switch( (*p) ) { - case 65: goto tr624; - case 67: goto tr624; - case 71: goto tr624; - case 78: goto tr624; - case 84: goto tr624; - case 97: goto tr624; - case 99: goto tr624; - case 103: goto tr624; - case 110: goto tr624; - case 116: goto tr624; - } - goto tr623; -tr624: +#line 10165 "vcf_validator_detail.hpp" + switch( (*p) ) { + case 65: goto tr628; + case 67: goto tr628; + case 71: goto tr628; + case 78: goto tr628; + case 84: goto tr628; + case 97: goto tr628; + case 99: goto tr628; + case 103: goto tr628; + case 110: goto tr628; + case 116: goto tr628; + } + goto tr627; +tr628: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10087,9 +10185,9 @@ case 551: if ( ++p == pe ) goto _test_eof552; case 552: -#line 10091 "vcf_validator_detail.hpp" +#line 10189 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr625; + case 9: goto tr629; case 65: goto st552; case 67: goto st552; case 71: goto st552; @@ -10101,8 +10199,8 @@ case 552: case 110: goto st552; case 116: goto st552; } - goto tr623; -tr625: + goto tr627; +tr629: #line 157 "vcf_v41.ragel" { // set_vcf_record_reference(ts, p-ts, status->current_record); @@ -10116,27 +10214,27 @@ case 552: if ( ++p == pe ) goto _test_eof553; case 553: -#line 10120 "vcf_validator_detail.hpp" - switch( (*p) ) { - case 42: goto tr628; - case 46: goto tr629; - case 48: goto tr630; - case 60: goto tr631; - case 65: goto tr632; - case 67: goto tr632; - case 71: goto tr632; - case 78: goto tr632; - case 84: goto tr632; - case 91: goto tr633; - case 93: goto tr634; - case 97: goto tr632; - case 99: goto tr632; - case 103: goto tr632; - case 110: goto tr632; - case 116: goto tr632; - } - goto tr627; -tr628: +#line 10218 "vcf_validator_detail.hpp" + switch( (*p) ) { + case 42: goto tr632; + case 46: goto tr633; + case 48: goto tr634; + case 60: goto tr635; + case 65: goto tr636; + case 67: goto tr636; + case 71: goto tr636; + case 78: goto tr636; + case 84: goto tr636; + case 91: goto tr637; + case 93: goto tr638; + case 97: goto tr636; + case 99: goto tr636; + case 103: goto tr636; + case 110: goto tr636; + case 116: goto tr636; + } + goto tr631; +tr632: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10146,11 +10244,11 @@ case 553: if ( ++p == pe ) goto _test_eof554; case 554: -#line 10150 "vcf_validator_detail.hpp" +#line 10248 "vcf_validator_detail.hpp" if ( (*p) == 9 ) - goto tr635; - goto tr627; -tr635: + goto tr639; + goto tr631; +tr639: #line 173 "vcf_v41.ragel" { // set_vcf_record_type(VARIANT_INDEL, status->current_record); @@ -10168,7 +10266,7 @@ case 554: ++n_columns; } goto st555; -tr744: +tr748: #line 169 "vcf_v41.ragel" { // set_vcf_record_type(VARIANT_SNV, status->current_record); @@ -10186,7 +10284,7 @@ case 554: ++n_columns; } goto st555; -tr746: +tr750: #line 177 "vcf_v41.ragel" { // set_vcf_record_type(VARIANT_SV, status->current_record); @@ -10204,7 +10302,7 @@ case 554: ++n_columns; } goto st555; -tr755: +tr759: #line 161 "vcf_v41.ragel" { /* if (!strncmp("0", ts, 1)) { @@ -10222,13 +10320,13 @@ case 554: if ( ++p == pe ) goto _test_eof555; case 555: -#line 10226 "vcf_validator_detail.hpp" +#line 10324 "vcf_validator_detail.hpp" if ( (*p) == 46 ) - goto tr637; + goto tr641; if ( 48 <= (*p) && (*p) <= 57 ) - goto tr638; - goto tr636; -tr637: + goto tr642; + goto tr640; +tr641: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10238,11 +10336,11 @@ case 555: if ( ++p == pe ) goto _test_eof556; case 556: -#line 10242 "vcf_validator_detail.hpp" +#line 10340 "vcf_validator_detail.hpp" if ( (*p) == 9 ) - goto tr639; - goto tr636; -tr639: + goto tr643; + goto tr640; +tr643: #line 181 "vcf_v41.ragel" { /* float quality = -1.0f; @@ -10262,14 +10360,14 @@ case 556: if ( ++p == pe ) goto _test_eof557; case 557: -#line 10266 "vcf_validator_detail.hpp" +#line 10364 "vcf_validator_detail.hpp" if ( (*p) > 58 ) { if ( 60 <= (*p) && (*p) <= 126 ) - goto tr641; + goto tr645; } else if ( (*p) >= 33 ) - goto tr641; - goto tr640; -tr641: + goto tr645; + goto tr644; +tr645: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10279,15 +10377,15 @@ case 557: if ( ++p == pe ) goto _test_eof558; case 558: -#line 10283 "vcf_validator_detail.hpp" +#line 10381 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr642; + case 9: goto tr646; case 59: goto st633; } if ( 33 <= (*p) && (*p) <= 126 ) goto st558; - goto tr640; -tr642: + goto tr644; +tr646: #line 191 "vcf_v41.ragel" { // set_vcf_record_filter(ts, p-ts, status->current_record); @@ -10301,32 +10399,32 @@ case 558: if ( ++p == pe ) goto _test_eof559; case 559: -#line 10305 "vcf_validator_detail.hpp" - switch( (*p) ) { - case 46: goto tr646; - case 49: goto tr648; - case 65: goto tr649; - case 66: goto tr650; - case 67: goto tr651; - case 68: goto tr652; - case 69: goto tr653; - case 72: goto tr654; - case 77: goto tr655; - case 78: goto tr656; - case 83: goto tr657; - case 86: goto tr658; - case 95: goto tr647; +#line 10403 "vcf_validator_detail.hpp" + switch( (*p) ) { + case 46: goto tr650; + case 49: goto tr652; + case 65: goto tr653; + case 66: goto tr654; + case 67: goto tr655; + case 68: goto tr656; + case 69: goto tr657; + case 72: goto tr658; + case 77: goto tr659; + case 78: goto tr660; + case 83: goto tr661; + case 86: goto tr662; + case 95: goto tr651; } if ( (*p) < 70 ) { if ( 48 <= (*p) && (*p) <= 57 ) - goto tr647; + goto tr651; } else if ( (*p) > 90 ) { if ( 97 <= (*p) && (*p) <= 122 ) - goto tr647; + goto tr651; } else - goto tr647; - goto tr645; -tr646: + goto tr651; + goto tr649; +tr650: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10336,15 +10434,15 @@ case 559: if ( ++p == pe ) goto _test_eof560; case 560: -#line 10340 "vcf_validator_detail.hpp" +#line 10438 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; } - goto tr645; -tr659: + goto tr649; +tr663: #line 195 "vcf_v41.ragel" { // set_vcf_record_info(ts, p-ts, status->current_record); @@ -10358,22 +10456,22 @@ case 560: if ( ++p == pe ) goto _test_eof561; case 561: -#line 10362 "vcf_validator_detail.hpp" +#line 10460 "vcf_validator_detail.hpp" switch( (*p) ) { - case 45: goto tr664; - case 46: goto tr665; - case 95: goto tr667; + case 45: goto tr668; + case 46: goto tr669; + case 95: goto tr671; } if ( (*p) < 65 ) { if ( 48 <= (*p) && (*p) <= 57 ) - goto tr666; + goto tr670; } else if ( (*p) > 90 ) { if ( 97 <= (*p) && (*p) <= 122 ) - goto tr666; + goto tr670; } else - goto tr666; - goto tr663; -tr664: + goto tr670; + goto tr667; +tr668: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10383,7 +10481,7 @@ case 561: if ( ++p == pe ) goto _test_eof562; case 562: -#line 10387 "vcf_validator_detail.hpp" +#line 10485 "vcf_validator_detail.hpp" switch( (*p) ) { case 45: goto st562; case 46: goto st563; @@ -10397,8 +10495,8 @@ case 562: goto st563; } else goto st563; - goto tr663; -tr666: + goto tr667; +tr670: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10408,9 +10506,9 @@ case 562: if ( ++p == pe ) goto _test_eof563; case 563: -#line 10412 "vcf_validator_detail.hpp" +#line 10510 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr670; + case 9: goto tr674; case 58: goto st572; case 95: goto st563; } @@ -10425,8 +10523,8 @@ case 563: goto st563; } else goto st563; - goto tr663; -tr670: + goto tr667; +tr674: #line 199 "vcf_v41.ragel" { // set_vcf_record_format(ts, p-ts, status->current_record); @@ -10436,7 +10534,7 @@ case 563: ++n_columns; } goto st564; -tr674: +tr678: #line 203 "vcf_v41.ragel" { // add_vcf_record_sample(ts, p-ts, status->current_record); @@ -10450,13 +10548,13 @@ case 563: if ( ++p == pe ) goto _test_eof564; case 564: -#line 10454 "vcf_validator_detail.hpp" +#line 10552 "vcf_validator_detail.hpp" if ( (*p) == 46 ) - goto tr673; + goto tr677; if ( 48 <= (*p) && (*p) <= 57 ) - goto tr673; - goto tr672; -tr673: + goto tr677; + goto tr676; +tr677: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10466,16 +10564,16 @@ case 564: if ( ++p == pe ) goto _test_eof565; case 565: -#line 10470 "vcf_validator_detail.hpp" +#line 10568 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr674; - case 10: goto tr675; + case 9: goto tr678; + case 10: goto tr679; case 47: goto st569; case 58: goto st570; case 124: goto st569; } - goto tr672; -tr660: + goto tr676; +tr664: #line 195 "vcf_v41.ragel" { // set_vcf_record_info(ts, p-ts, status->current_record); @@ -10510,7 +10608,7 @@ case 565: n_columns = 1; } goto st705; -tr675: +tr679: #line 203 "vcf_v41.ragel" { // add_vcf_record_sample(ts, p-ts, status->current_record); @@ -10549,19 +10647,19 @@ case 565: if ( ++p == pe ) goto _test_eof705; case 705: -#line 10553 "vcf_validator_detail.hpp" +#line 10651 "vcf_validator_detail.hpp" if ( (*p) == 60 ) - goto tr813; + goto tr817; if ( (*p) < 59 ) { if ( 33 <= (*p) && (*p) <= 57 ) - goto tr812; + goto tr816; } else if ( (*p) > 61 ) { if ( 63 <= (*p) && (*p) <= 126 ) - goto tr812; + goto tr816; } else - goto tr812; - goto tr611; -tr813: + goto tr816; + goto tr615; +tr817: #line 114 "vcf_v41.ragel" { // status->current_record = vcf_record_new(); @@ -10576,7 +10674,7 @@ case 705: if ( ++p == pe ) goto _test_eof566; case 566: -#line 10580 "vcf_validator_detail.hpp" +#line 10678 "vcf_validator_detail.hpp" if ( (*p) < 59 ) { if ( 33 <= (*p) && (*p) <= 57 ) goto st567; @@ -10585,7 +10683,7 @@ case 566: goto st567; } else goto st567; - goto tr611; + goto tr615; st567: if ( ++p == pe ) goto _test_eof567; @@ -10597,14 +10695,14 @@ case 567: goto st567; } else if ( (*p) >= 33 ) goto st567; - goto tr611; + goto tr615; st568: if ( ++p == pe ) goto _test_eof568; case 568: if ( (*p) == 9 ) - goto tr612; - goto tr611; + goto tr616; + goto tr615; st569: if ( ++p == pe ) goto _test_eof569; @@ -10613,25 +10711,25 @@ case 569: goto st565; if ( 48 <= (*p) && (*p) <= 57 ) goto st565; - goto tr672; + goto tr676; st570: if ( ++p == pe ) goto _test_eof570; case 570: if ( 33 <= (*p) && (*p) <= 126 ) goto st571; - goto tr672; + goto tr676; st571: if ( ++p == pe ) goto _test_eof571; case 571: switch( (*p) ) { - case 9: goto tr674; - case 10: goto tr675; + case 9: goto tr678; + case 10: goto tr679; } if ( 33 <= (*p) && (*p) <= 126 ) goto st571; - goto tr672; + goto tr676; st572: if ( ++p == pe ) goto _test_eof572; @@ -10649,8 +10747,8 @@ case 572: goto st563; } else goto st563; - goto tr663; -tr665: + goto tr667; +tr669: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10660,7 +10758,7 @@ case 572: if ( ++p == pe ) goto _test_eof573; case 573: -#line 10664 "vcf_validator_detail.hpp" +#line 10762 "vcf_validator_detail.hpp" switch( (*p) ) { case 45: goto st563; case 46: goto st573; @@ -10674,8 +10772,8 @@ case 573: goto st563; } else goto st563; - goto tr663; -tr667: + goto tr667; +tr671: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10685,7 +10783,7 @@ case 573: if ( ++p == pe ) goto _test_eof574; case 574: -#line 10689 "vcf_validator_detail.hpp" +#line 10787 "vcf_validator_detail.hpp" if ( (*p) == 95 ) goto st574; if ( (*p) < 48 ) { @@ -10699,7 +10797,7 @@ case 574: goto st563; } else goto st563; - goto tr663; + goto tr667; st575: if ( ++p == pe ) goto _test_eof575; @@ -10727,8 +10825,8 @@ case 575: goto st576; } else goto st576; - goto tr645; -tr647: + goto tr649; +tr651: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10738,10 +10836,10 @@ case 575: if ( ++p == pe ) goto _test_eof576; case 576: -#line 10742 "vcf_validator_detail.hpp" +#line 10840 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 95: goto st576; @@ -10754,26 +10852,26 @@ case 576: goto st576; } else goto st576; - goto tr645; + goto tr649; st577: if ( ++p == pe ) goto _test_eof577; case 577: if ( 33 <= (*p) && (*p) <= 126 ) goto st578; - goto tr645; + goto tr649; st578: if ( ++p == pe ) goto _test_eof578; case 578: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; } if ( 33 <= (*p) && (*p) <= 126 ) goto st578; - goto tr645; -tr648: + goto tr649; +tr652: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10783,10 +10881,10 @@ case 578: if ( ++p == pe ) goto _test_eof579; case 579: -#line 10787 "vcf_validator_detail.hpp" +#line 10885 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 48: goto st580; case 59: goto st575; case 61: goto st577; @@ -10800,14 +10898,14 @@ case 579: goto st576; } else goto st576; - goto tr645; + goto tr649; st580: if ( ++p == pe ) goto _test_eof580; case 580: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 48: goto st581; case 59: goto st575; case 61: goto st577; @@ -10821,14 +10919,14 @@ case 580: goto st576; } else goto st576; - goto tr645; + goto tr649; st581: if ( ++p == pe ) goto _test_eof581; case 581: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 48: goto st582; case 59: goto st575; case 61: goto st577; @@ -10842,14 +10940,14 @@ case 581: goto st576; } else goto st576; - goto tr645; + goto tr649; st582: if ( ++p == pe ) goto _test_eof582; case 582: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 71: goto st583; @@ -10863,14 +10961,14 @@ case 582: goto st576; } else goto st576; - goto tr645; + goto tr649; st583: if ( ++p == pe ) goto _test_eof583; case 583: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st584; case 95: goto st576; @@ -10883,25 +10981,25 @@ case 583: goto st576; } else goto st576; - goto tr645; + goto tr649; st584: if ( ++p == pe ) goto _test_eof584; case 584: if ( 48 <= (*p) && (*p) <= 49 ) goto st585; - goto tr645; + goto tr649; st585: if ( ++p == pe ) goto _test_eof585; case 585: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; } - goto tr645; -tr649: + goto tr649; +tr653: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -10911,10 +11009,10 @@ case 585: if ( ++p == pe ) goto _test_eof586; case 586: -#line 10915 "vcf_validator_detail.hpp" +#line 11013 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 65: goto st587; @@ -10931,7 +11029,7 @@ case 586: goto st576; } else goto st576; - goto tr645; + goto tr649; st587: if ( ++p == pe ) goto _test_eof587; @@ -10948,7 +11046,7 @@ case 587: goto st576; } else goto st576; - goto tr645; + goto tr649; st588: if ( ++p == pe ) goto _test_eof588; @@ -10966,14 +11064,14 @@ case 588: case 110: goto st589; case 116: goto st589; } - goto tr645; + goto tr649; st589: if ( ++p == pe ) goto _test_eof589; case 589: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 65: goto st589; case 67: goto st589; @@ -10986,7 +11084,7 @@ case 589: case 110: goto st589; case 116: goto st589; } - goto tr645; + goto tr649; st590: if ( ++p == pe ) goto _test_eof590; @@ -11003,27 +11101,27 @@ case 590: goto st576; } else goto st576; - goto tr645; + goto tr649; st591: if ( ++p == pe ) goto _test_eof591; case 591: if ( 48 <= (*p) && (*p) <= 57 ) goto st592; - goto tr645; + goto tr649; st592: if ( ++p == pe ) goto _test_eof592; case 592: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 44: goto st591; case 59: goto st575; } if ( 48 <= (*p) && (*p) <= 57 ) goto st592; - goto tr645; + goto tr649; st593: if ( ++p == pe ) goto _test_eof593; @@ -11040,48 +11138,48 @@ case 593: goto st576; } else goto st576; - goto tr645; + goto tr649; st594: if ( ++p == pe ) goto _test_eof594; case 594: if ( 48 <= (*p) && (*p) <= 57 ) goto st595; - goto tr645; + goto tr649; st595: if ( ++p == pe ) goto _test_eof595; case 595: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 44: goto st594; case 46: goto st596; case 59: goto st575; } if ( 48 <= (*p) && (*p) <= 57 ) goto st595; - goto tr645; + goto tr649; st596: if ( ++p == pe ) goto _test_eof596; case 596: if ( 48 <= (*p) && (*p) <= 57 ) goto st597; - goto tr645; + goto tr649; st597: if ( ++p == pe ) goto _test_eof597; case 597: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 44: goto st594; case 59: goto st575; } if ( 48 <= (*p) && (*p) <= 57 ) goto st597; - goto tr645; + goto tr649; st598: if ( ++p == pe ) goto _test_eof598; @@ -11098,27 +11196,27 @@ case 598: goto st576; } else goto st576; - goto tr645; + goto tr649; st599: if ( ++p == pe ) goto _test_eof599; case 599: if ( 48 <= (*p) && (*p) <= 57 ) goto st600; - goto tr645; + goto tr649; st600: if ( ++p == pe ) goto _test_eof600; case 600: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; } if ( 48 <= (*p) && (*p) <= 57 ) goto st600; - goto tr645; -tr650: + goto tr649; +tr654: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11128,10 +11226,10 @@ case 600: if ( ++p == pe ) goto _test_eof601; case 601: -#line 11132 "vcf_validator_detail.hpp" +#line 11230 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 81: goto st602; @@ -11145,7 +11243,7 @@ case 601: goto st576; } else goto st576; - goto tr645; + goto tr649; st602: if ( ++p == pe ) goto _test_eof602; @@ -11162,28 +11260,28 @@ case 602: goto st576; } else goto st576; - goto tr645; + goto tr649; st603: if ( ++p == pe ) goto _test_eof603; case 603: if ( 48 <= (*p) && (*p) <= 57 ) goto st604; - goto tr645; + goto tr649; st604: if ( ++p == pe ) goto _test_eof604; case 604: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 46: goto st599; case 59: goto st575; } if ( 48 <= (*p) && (*p) <= 57 ) goto st604; - goto tr645; -tr651: + goto tr649; +tr655: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11193,10 +11291,10 @@ case 604: if ( ++p == pe ) goto _test_eof605; case 605: -#line 11197 "vcf_validator_detail.hpp" +#line 11295 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 73: goto st606; @@ -11210,14 +11308,14 @@ case 605: goto st576; } else goto st576; - goto tr645; + goto tr649; st606: if ( ++p == pe ) goto _test_eof606; case 606: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 71: goto st607; @@ -11231,14 +11329,14 @@ case 606: goto st576; } else goto st576; - goto tr645; + goto tr649; st607: if ( ++p == pe ) goto _test_eof607; case 607: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 65: goto st608; @@ -11252,14 +11350,14 @@ case 607: goto st576; } else goto st576; - goto tr645; + goto tr649; st608: if ( ++p == pe ) goto _test_eof608; case 608: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 82: goto st609; @@ -11273,7 +11371,7 @@ case 608: goto st576; } else goto st576; - goto tr645; + goto tr649; st609: if ( ++p == pe ) goto _test_eof609; @@ -11290,7 +11388,7 @@ case 609: goto st576; } else goto st576; - goto tr645; + goto tr649; st610: if ( ++p == pe ) goto _test_eof610; @@ -11303,14 +11401,14 @@ case 610: goto st611; } else goto st611; - goto tr645; + goto tr649; st611: if ( ++p == pe ) goto _test_eof611; case 611: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; } if ( (*p) < 65 ) { @@ -11321,8 +11419,8 @@ case 611: goto st611; } else goto st611; - goto tr645; -tr652: + goto tr649; +tr656: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11332,10 +11430,10 @@ case 611: if ( ++p == pe ) goto _test_eof612; case 612: -#line 11336 "vcf_validator_detail.hpp" +#line 11434 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 66: goto st583; @@ -11350,8 +11448,8 @@ case 612: goto st576; } else goto st576; - goto tr645; -tr653: + goto tr649; +tr657: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11361,10 +11459,10 @@ case 612: if ( ++p == pe ) goto _test_eof613; case 613: -#line 11365 "vcf_validator_detail.hpp" +#line 11463 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 78: goto st614; @@ -11378,14 +11476,14 @@ case 613: goto st576; } else goto st576; - goto tr645; + goto tr649; st614: if ( ++p == pe ) goto _test_eof614; case 614: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 68: goto st598; @@ -11399,8 +11497,8 @@ case 614: goto st576; } else goto st576; - goto tr645; -tr654: + goto tr649; +tr658: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11410,10 +11508,10 @@ case 614: if ( ++p == pe ) goto _test_eof615; case 615: -#line 11414 "vcf_validator_detail.hpp" +#line 11512 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 95: goto st576; @@ -11432,8 +11530,8 @@ case 615: goto st576; } else goto st576; - goto tr645; -tr655: + goto tr649; +tr659: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11443,10 +11541,10 @@ case 615: if ( ++p == pe ) goto _test_eof616; case 616: -#line 11447 "vcf_validator_detail.hpp" +#line 11545 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 81: goto st617; @@ -11460,7 +11558,7 @@ case 616: goto st576; } else goto st576; - goto tr645; + goto tr649; st617: if ( ++p == pe ) goto _test_eof617; @@ -11478,8 +11576,8 @@ case 617: goto st576; } else goto st576; - goto tr645; -tr656: + goto tr649; +tr660: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11489,10 +11587,10 @@ case 617: if ( ++p == pe ) goto _test_eof618; case 618: -#line 11493 "vcf_validator_detail.hpp" +#line 11591 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 83: goto st598; @@ -11506,8 +11604,8 @@ case 618: goto st576; } else goto st576; - goto tr645; -tr657: + goto tr649; +tr661: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11517,10 +11615,10 @@ case 618: if ( ++p == pe ) goto _test_eof619; case 619: -#line 11521 "vcf_validator_detail.hpp" +#line 11619 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 66: goto st602; @@ -11535,14 +11633,14 @@ case 619: goto st576; } else goto st576; - goto tr645; + goto tr649; st620: if ( ++p == pe ) goto _test_eof620; case 620: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 77: goto st621; @@ -11556,14 +11654,14 @@ case 620: goto st576; } else goto st576; - goto tr645; + goto tr649; st621: if ( ++p == pe ) goto _test_eof621; case 621: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 65: goto st622; @@ -11577,14 +11675,14 @@ case 621: goto st576; } else goto st576; - goto tr645; + goto tr649; st622: if ( ++p == pe ) goto _test_eof622; case 622: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 84: goto st623; @@ -11598,14 +11696,14 @@ case 622: goto st576; } else goto st576; - goto tr645; + goto tr649; st623: if ( ++p == pe ) goto _test_eof623; case 623: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 73: goto st624; @@ -11619,14 +11717,14 @@ case 623: goto st576; } else goto st576; - goto tr645; + goto tr649; st624: if ( ++p == pe ) goto _test_eof624; case 624: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 67: goto st583; @@ -11640,8 +11738,8 @@ case 624: goto st576; } else goto st576; - goto tr645; -tr658: + goto tr649; +tr662: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11651,10 +11749,10 @@ case 624: if ( ++p == pe ) goto _test_eof625; case 625: -#line 11655 "vcf_validator_detail.hpp" +#line 11753 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 65: goto st626; @@ -11668,14 +11766,14 @@ case 625: goto st576; } else goto st576; - goto tr645; + goto tr649; st626: if ( ++p == pe ) goto _test_eof626; case 626: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 76: goto st627; @@ -11689,14 +11787,14 @@ case 626: goto st576; } else goto st576; - goto tr645; + goto tr649; st627: if ( ++p == pe ) goto _test_eof627; case 627: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 73: goto st628; @@ -11710,14 +11808,14 @@ case 627: goto st576; } else goto st576; - goto tr645; + goto tr649; st628: if ( ++p == pe ) goto _test_eof628; case 628: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 68: goto st629; @@ -11731,14 +11829,14 @@ case 628: goto st576; } else goto st576; - goto tr645; + goto tr649; st629: if ( ++p == pe ) goto _test_eof629; case 629: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 65: goto st630; @@ -11752,14 +11850,14 @@ case 629: goto st576; } else goto st576; - goto tr645; + goto tr649; st630: if ( ++p == pe ) goto _test_eof630; case 630: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 84: goto st631; @@ -11773,14 +11871,14 @@ case 630: goto st576; } else goto st576; - goto tr645; + goto tr649; st631: if ( ++p == pe ) goto _test_eof631; case 631: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 69: goto st632; @@ -11794,14 +11892,14 @@ case 631: goto st576; } else goto st576; - goto tr645; + goto tr649; st632: if ( ++p == pe ) goto _test_eof632; case 632: switch( (*p) ) { - case 9: goto tr659; - case 10: goto tr660; + case 9: goto tr663; + case 10: goto tr664; case 59: goto st575; case 61: goto st577; case 68: goto st583; @@ -11815,7 +11913,7 @@ case 632: goto st576; } else goto st576; - goto tr645; + goto tr649; st633: if ( ++p == pe ) goto _test_eof633; @@ -11825,8 +11923,8 @@ case 633: goto st558; } else if ( (*p) >= 33 ) goto st558; - goto tr640; -tr638: + goto tr644; +tr642: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11836,31 +11934,31 @@ case 633: if ( ++p == pe ) goto _test_eof634; case 634: -#line 11840 "vcf_validator_detail.hpp" +#line 11938 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr639; + case 9: goto tr643; case 46: goto st635; } if ( 48 <= (*p) && (*p) <= 57 ) goto st634; - goto tr636; + goto tr640; st635: if ( ++p == pe ) goto _test_eof635; case 635: if ( 48 <= (*p) && (*p) <= 57 ) goto st636; - goto tr636; + goto tr640; st636: if ( ++p == pe ) goto _test_eof636; case 636: if ( (*p) == 9 ) - goto tr639; + goto tr643; if ( 48 <= (*p) && (*p) <= 57 ) goto st636; - goto tr636; -tr629: + goto tr640; +tr633: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11870,9 +11968,9 @@ case 636: if ( ++p == pe ) goto _test_eof637; case 637: -#line 11874 "vcf_validator_detail.hpp" +#line 11972 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr744; + case 9: goto tr748; case 65: goto st638; case 67: goto st638; case 71: goto st638; @@ -11884,13 +11982,13 @@ case 637: case 110: goto st638; case 116: goto st638; } - goto tr627; + goto tr631; st638: if ( ++p == pe ) goto _test_eof638; case 638: switch( (*p) ) { - case 9: goto tr746; + case 9: goto tr750; case 65: goto st638; case 67: goto st638; case 71: goto st638; @@ -11902,8 +12000,8 @@ case 638: case 110: goto st638; case 116: goto st638; } - goto tr627; -tr630: + goto tr631; +tr634: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11913,11 +12011,11 @@ case 638: if ( ++p == pe ) goto _test_eof639; case 639: -#line 11917 "vcf_validator_detail.hpp" +#line 12015 "vcf_validator_detail.hpp" if ( (*p) == 9 ) - goto tr744; - goto tr627; -tr631: + goto tr748; + goto tr631; +tr635: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -11927,7 +12025,7 @@ case 639: if ( ++p == pe ) goto _test_eof640; case 640: -#line 11931 "vcf_validator_detail.hpp" +#line 12029 "vcf_validator_detail.hpp" switch( (*p) ) { case 45: goto st641; case 46: goto st644; @@ -11944,7 +12042,7 @@ case 640: goto st642; } else goto st642; - goto tr627; + goto tr631; st641: if ( ++p == pe ) goto _test_eof641; @@ -11962,7 +12060,7 @@ case 641: goto st642; } else goto st642; - goto tr627; + goto tr631; st642: if ( ++p == pe ) goto _test_eof642; @@ -11982,14 +12080,14 @@ case 642: goto st642; } else goto st642; - goto tr627; + goto tr631; st643: if ( ++p == pe ) goto _test_eof643; case 643: if ( (*p) == 9 ) - goto tr755; - goto tr627; + goto tr759; + goto tr631; st644: if ( ++p == pe ) goto _test_eof644; @@ -12007,7 +12105,7 @@ case 644: goto st642; } else goto st642; - goto tr627; + goto tr631; st645: if ( ++p == pe ) goto _test_eof645; @@ -12028,7 +12126,7 @@ case 645: goto st642; } else goto st642; - goto tr627; + goto tr631; st646: if ( ++p == pe ) goto _test_eof646; @@ -12049,7 +12147,7 @@ case 646: goto st642; } else goto st642; - goto tr627; + goto tr631; st647: if ( ++p == pe ) goto _test_eof647; @@ -12069,7 +12167,7 @@ case 647: goto st642; } else goto st642; - goto tr627; + goto tr631; st648: if ( ++p == pe ) goto _test_eof648; @@ -12091,7 +12189,7 @@ case 648: goto st642; } else goto st642; - goto tr627; + goto tr631; st649: if ( ++p == pe ) goto _test_eof649; @@ -12112,7 +12210,7 @@ case 649: goto st642; } else goto st642; - goto tr627; + goto tr631; st650: if ( ++p == pe ) goto _test_eof650; @@ -12133,28 +12231,28 @@ case 650: goto st642; } else goto st642; - goto tr627; + goto tr631; st651: if ( ++p == pe ) goto _test_eof651; case 651: if ( (*p) == 77 ) goto st652; - goto tr627; + goto tr631; st652: if ( ++p == pe ) goto _test_eof652; case 652: if ( (*p) == 69 ) goto st653; - goto tr627; + goto tr631; st653: if ( ++p == pe ) goto _test_eof653; case 653: if ( (*p) == 58 ) goto st654; - goto tr627; + goto tr631; st654: if ( ++p == pe ) goto _test_eof654; @@ -12167,7 +12265,7 @@ case 654: goto st655; } else goto st655; - goto tr627; + goto tr631; st655: if ( ++p == pe ) goto _test_eof655; @@ -12182,7 +12280,7 @@ case 655: goto st655; } else goto st655; - goto tr627; + goto tr631; st656: if ( ++p == pe ) goto _test_eof656; @@ -12203,7 +12301,7 @@ case 656: goto st642; } else goto st642; - goto tr627; + goto tr631; st657: if ( ++p == pe ) goto _test_eof657; @@ -12224,56 +12322,56 @@ case 657: goto st642; } else goto st642; - goto tr627; + goto tr631; st658: if ( ++p == pe ) goto _test_eof658; case 658: if ( (*p) == 84 ) goto st659; - goto tr627; + goto tr631; st659: if ( ++p == pe ) goto _test_eof659; case 659: if ( (*p) == 65 ) goto st660; - goto tr627; + goto tr631; st660: if ( ++p == pe ) goto _test_eof660; case 660: if ( (*p) == 78 ) goto st661; - goto tr627; + goto tr631; st661: if ( ++p == pe ) goto _test_eof661; case 661: if ( (*p) == 68 ) goto st662; - goto tr627; + goto tr631; st662: if ( ++p == pe ) goto _test_eof662; case 662: if ( (*p) == 69 ) goto st663; - goto tr627; + goto tr631; st663: if ( ++p == pe ) goto _test_eof663; case 663: if ( (*p) == 77 ) goto st664; - goto tr627; + goto tr631; st664: if ( ++p == pe ) goto _test_eof664; case 664: if ( (*p) == 62 ) goto st554; - goto tr627; + goto tr631; st665: if ( ++p == pe ) goto _test_eof665; @@ -12294,7 +12392,7 @@ case 665: goto st642; } else goto st642; - goto tr627; + goto tr631; st666: if ( ++p == pe ) goto _test_eof666; @@ -12316,7 +12414,7 @@ case 666: goto st642; } else goto st642; - goto tr627; + goto tr631; st667: if ( ++p == pe ) goto _test_eof667; @@ -12334,8 +12432,8 @@ case 667: goto st642; } else goto st642; - goto tr627; -tr632: + goto tr631; +tr636: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -12345,9 +12443,9 @@ case 667: if ( ++p == pe ) goto _test_eof668; case 668: -#line 12349 "vcf_validator_detail.hpp" +#line 12447 "vcf_validator_detail.hpp" switch( (*p) ) { - case 9: goto tr744; + case 9: goto tr748; case 44: goto st669; case 46: goto st671; case 65: goto st668; @@ -12363,7 +12461,7 @@ case 668: case 110: goto st668; case 116: goto st668; } - goto tr627; + goto tr631; st669: if ( ++p == pe ) goto _test_eof669; @@ -12380,13 +12478,13 @@ case 669: case 110: goto st670; case 116: goto st670; } - goto tr627; + goto tr631; st670: if ( ++p == pe ) goto _test_eof670; case 670: switch( (*p) ) { - case 9: goto tr744; + case 9: goto tr748; case 44: goto st669; case 65: goto st670; case 67: goto st670; @@ -12399,14 +12497,14 @@ case 670: case 110: goto st670; case 116: goto st670; } - goto tr627; + goto tr631; st671: if ( ++p == pe ) goto _test_eof671; case 671: if ( (*p) == 9 ) - goto tr746; - goto tr627; + goto tr750; + goto tr631; st672: if ( ++p == pe ) goto _test_eof672; @@ -12421,7 +12519,7 @@ case 672: goto st673; } else goto st673; - goto tr627; + goto tr631; st673: if ( ++p == pe ) goto _test_eof673; @@ -12435,14 +12533,14 @@ case 673: goto st673; } else if ( (*p) >= 33 ) goto st673; - goto tr627; + goto tr631; st674: if ( ++p == pe ) goto _test_eof674; case 674: if ( 48 <= (*p) && (*p) <= 57 ) goto st675; - goto tr627; + goto tr631; st675: if ( ++p == pe ) goto _test_eof675; @@ -12451,7 +12549,7 @@ case 675: goto st671; if ( 48 <= (*p) && (*p) <= 57 ) goto st675; - goto tr627; + goto tr631; st676: if ( ++p == pe ) goto _test_eof676; @@ -12464,7 +12562,7 @@ case 676: goto st677; } else goto st677; - goto tr627; + goto tr631; st677: if ( ++p == pe ) goto _test_eof677; @@ -12476,14 +12574,14 @@ case 677: goto st677; } else if ( (*p) >= 33 ) goto st677; - goto tr627; + goto tr631; st678: if ( ++p == pe ) goto _test_eof678; case 678: if ( (*p) == 58 ) goto st674; - goto tr627; + goto tr631; st679: if ( ++p == pe ) goto _test_eof679; @@ -12498,7 +12596,7 @@ case 679: goto st680; } else goto st680; - goto tr627; + goto tr631; st680: if ( ++p == pe ) goto _test_eof680; @@ -12512,14 +12610,14 @@ case 680: goto st680; } else if ( (*p) >= 33 ) goto st680; - goto tr627; + goto tr631; st681: if ( ++p == pe ) goto _test_eof681; case 681: if ( 48 <= (*p) && (*p) <= 57 ) goto st682; - goto tr627; + goto tr631; st682: if ( ++p == pe ) goto _test_eof682; @@ -12528,7 +12626,7 @@ case 682: goto st671; if ( 48 <= (*p) && (*p) <= 57 ) goto st682; - goto tr627; + goto tr631; st683: if ( ++p == pe ) goto _test_eof683; @@ -12541,7 +12639,7 @@ case 683: goto st684; } else goto st684; - goto tr627; + goto tr631; st684: if ( ++p == pe ) goto _test_eof684; @@ -12553,15 +12651,15 @@ case 684: goto st684; } else if ( (*p) >= 33 ) goto st684; - goto tr627; + goto tr631; st685: if ( ++p == pe ) goto _test_eof685; case 685: if ( (*p) == 58 ) goto st681; - goto tr627; -tr633: + goto tr631; +tr637: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -12571,7 +12669,7 @@ case 685: if ( ++p == pe ) goto _test_eof686; case 686: -#line 12575 "vcf_validator_detail.hpp" +#line 12673 "vcf_validator_detail.hpp" if ( (*p) == 60 ) goto st691; if ( (*p) < 59 ) { @@ -12582,7 +12680,7 @@ case 686: goto st687; } else goto st687; - goto tr627; + goto tr631; st687: if ( ++p == pe ) goto _test_eof687; @@ -12596,14 +12694,14 @@ case 687: goto st687; } else if ( (*p) >= 33 ) goto st687; - goto tr627; + goto tr631; st688: if ( ++p == pe ) goto _test_eof688; case 688: if ( 48 <= (*p) && (*p) <= 57 ) goto st689; - goto tr627; + goto tr631; st689: if ( ++p == pe ) goto _test_eof689; @@ -12612,7 +12710,7 @@ case 689: goto st690; if ( 48 <= (*p) && (*p) <= 57 ) goto st689; - goto tr627; + goto tr631; st690: if ( ++p == pe ) goto _test_eof690; @@ -12629,7 +12727,7 @@ case 690: case 110: goto st638; case 116: goto st638; } - goto tr627; + goto tr631; st691: if ( ++p == pe ) goto _test_eof691; @@ -12642,7 +12740,7 @@ case 691: goto st692; } else goto st692; - goto tr627; + goto tr631; st692: if ( ++p == pe ) goto _test_eof692; @@ -12654,15 +12752,15 @@ case 692: goto st692; } else if ( (*p) >= 33 ) goto st692; - goto tr627; + goto tr631; st693: if ( ++p == pe ) goto _test_eof693; case 693: if ( (*p) == 58 ) goto st688; - goto tr627; -tr634: + goto tr631; +tr638: #line 15 "vcf_v41.ragel" { ParsePolicy::handle_token_begin(*this); @@ -12672,7 +12770,7 @@ case 693: if ( ++p == pe ) goto _test_eof694; case 694: -#line 12676 "vcf_validator_detail.hpp" +#line 12774 "vcf_validator_detail.hpp" if ( (*p) == 60 ) goto st698; if ( (*p) < 59 ) { @@ -12683,7 +12781,7 @@ case 694: goto st695; } else goto st695; - goto tr627; + goto tr631; st695: if ( ++p == pe ) goto _test_eof695; @@ -12697,14 +12795,14 @@ case 695: goto st695; } else if ( (*p) >= 33 ) goto st695; - goto tr627; + goto tr631; st696: if ( ++p == pe ) goto _test_eof696; case 696: if ( 48 <= (*p) && (*p) <= 57 ) goto st697; - goto tr627; + goto tr631; st697: if ( ++p == pe ) goto _test_eof697; @@ -12713,7 +12811,7 @@ case 697: goto st690; if ( 48 <= (*p) && (*p) <= 57 ) goto st697; - goto tr627; + goto tr631; st698: if ( ++p == pe ) goto _test_eof698; @@ -12726,7 +12824,7 @@ case 698: goto st699; } else goto st699; - goto tr627; + goto tr631; st699: if ( ++p == pe ) goto _test_eof699; @@ -12738,14 +12836,14 @@ case 699: goto st699; } else if ( (*p) >= 33 ) goto st699; - goto tr627; + goto tr631; st700: if ( ++p == pe ) goto _test_eof700; case 700: if ( (*p) == 58 ) goto st696; - goto tr627; + goto tr631; st701: if ( ++p == pe ) goto _test_eof701; @@ -12755,50 +12853,50 @@ case 701: goto st550; } else if ( (*p) >= 33 ) goto st550; - goto tr618; + goto tr622; st702: if ( ++p == pe ) goto _test_eof702; case 702: if ( (*p) == 10 ) - goto tr808; + goto tr812; goto st702; -tr808: +tr812: #line 23 "vcf_v41.ragel" { ++n_lines; n_columns = 1; } -#line 565 "vcf_v41.ragel" +#line 577 "vcf_v41.ragel" { {goto st20;} } goto st706; st706: if ( ++p == pe ) goto _test_eof706; case 706: -#line 12780 "vcf_validator_detail.hpp" +#line 12878 "vcf_validator_detail.hpp" goto st0; st703: if ( ++p == pe ) goto _test_eof703; case 703: if ( (*p) == 10 ) - goto tr810; + goto tr814; goto st703; -tr810: +tr814: #line 23 "vcf_v41.ragel" { ++n_lines; n_columns = 1; } -#line 566 "vcf_v41.ragel" +#line 578 "vcf_v41.ragel" { {goto st705;} } goto st707; st707: if ( ++p == pe ) goto _test_eof707; case 707: -#line 12802 "vcf_validator_detail.hpp" +#line 12900 "vcf_validator_detail.hpp" goto st0; } _test_eof2: cs = 2; goto _test_eof; @@ -13532,7 +13630,6 @@ case 707: } break; case 19: - case 491: #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -13643,7 +13740,7 @@ case 707: case 468: case 469: case 470: -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -13673,7 +13770,7 @@ case 707: case 194: case 195: case 198: -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -13715,7 +13812,7 @@ case 707: case 249: case 250: case 253: -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -13757,7 +13854,7 @@ case 707: case 317: case 318: case 344: -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -13770,11 +13867,23 @@ case 707: break; case 369: case 376: -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + break; + case 491: +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -13786,7 +13895,7 @@ case 707: case 389: case 390: case 432: -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -13898,55 +14007,11 @@ case 707: case 119: case 120: case 121: - case 439: - case 440: - case 441: - case 442: - case 443: - case 444: - case 445: - case 446: - case 481: - case 482: - case 483: - case 484: - case 485: - case 486: - case 487: - case 488: - case 489: - case 490: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 40 "vcf_v41.ragel" - { - ErrorPolicy::handle_meta_section_error(*this); - p--; {goto st702;} - } - break; - case 447: - case 448: - case 449: - case 450: - case 451: - case 452: - case 453: - case 492: - case 493: - case 494: - case 495: - case 496: - case 497: - case 498: - case 499: -#line 325 "vcf_v41.ragel" - { - ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); - p--; {goto st702;} - } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -13957,7 +14022,7 @@ case 707: case 566: case 567: case 568: -#line 332 "vcf_v41.ragel" +#line 344 "vcf_v41.ragel" { printf("Line %zu: Error in 'chrom' field\n", n_lines); p--; {goto st703;} @@ -13970,7 +14035,7 @@ case 707: break; case 547: case 548: -#line 337 "vcf_v41.ragel" +#line 349 "vcf_v41.ragel" { ErrorPolicy::handle_body_section_error(*this, "Position is not a positive number"); p--; {goto st703;} @@ -13984,7 +14049,7 @@ case 707: case 549: case 550: case 701: -#line 342 "vcf_v41.ragel" +#line 354 "vcf_v41.ragel" { printf("Line %zu: Error in 'id' field\n", n_lines); p--; {goto st703;} @@ -13997,7 +14062,7 @@ case 707: break; case 551: case 552: -#line 347 "vcf_v41.ragel" +#line 359 "vcf_v41.ragel" { printf("Line %zu: Error in 'reference' field\n", n_lines); p--; {goto st703;} @@ -14074,7 +14139,7 @@ case 707: case 698: case 699: case 700: -#line 352 "vcf_v41.ragel" +#line 364 "vcf_v41.ragel" { printf("Line %zu: Error in 'alternate' field\n", n_lines); p--; {goto st703;} @@ -14090,7 +14155,7 @@ case 707: case 634: case 635: case 636: -#line 357 "vcf_v41.ragel" +#line 369 "vcf_v41.ragel" { printf("Line %zu: Error in 'quality' field\n", n_lines); p--; {goto st703;} @@ -14104,7 +14169,7 @@ case 707: case 557: case 558: case 633: -#line 362 "vcf_v41.ragel" +#line 374 "vcf_v41.ragel" { printf("Line %zu: Error in 'filter' field\n", n_lines); p--; {goto st703;} @@ -14175,7 +14240,7 @@ case 707: case 630: case 631: case 632: -#line 367 "vcf_v41.ragel" +#line 379 "vcf_v41.ragel" { printf("Line %zu: Error in 'info' field\n", n_lines); p--; {goto st703;} @@ -14192,7 +14257,7 @@ case 707: case 572: case 573: case 574: -#line 372 "vcf_v41.ragel" +#line 384 "vcf_v41.ragel" { printf("Line %zu: Error in 'format' field\n", n_lines); p--; {goto st703;} @@ -14208,7 +14273,7 @@ case 707: case 569: case 570: case 571: -#line 377 "vcf_v41.ragel" +#line 389 "vcf_v41.ragel" { ErrorPolicy::handle_body_section_error(*this, "Incorrect sample format"); p--; {goto st703;} @@ -14276,12 +14341,12 @@ case 707: case 220: case 221: case 267: -#line 251 "vcf_v41.ragel" +#line 257 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "FORMAT metadata Number is not a number, A, R, G or dot"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -14315,12 +14380,12 @@ case 707: case 264: case 265: case 266: -#line 256 "vcf_v41.ragel" +#line 262 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "FORMAT metadata Type is not a Integer, Float, Character or String"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -14334,12 +14399,12 @@ case 707: case 288: case 289: case 358: -#line 267 "vcf_v41.ragel" +#line 273 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Number is not a number, A, R, G or dot"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14373,12 +14438,12 @@ case 707: case 355: case 356: case 357: -#line 272 "vcf_v41.ragel" +#line 278 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Type is not a Integer, Float, Flag, Character or String"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14398,12 +14463,12 @@ case 707: case 328: case 329: case 330: -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14426,12 +14491,12 @@ case 707: case 341: case 342: case 343: -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14454,12 +14519,12 @@ case 707: case 403: case 435: case 436: -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14482,12 +14547,12 @@ case 707: case 414: case 433: case 434: -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14501,7 +14566,7 @@ case 707: case 122: case 123: case 124: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -14511,6 +14576,30 @@ case 707: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + break; + case 439: + case 440: + case 441: + case 442: + case 443: + case 444: + case 445: + case 446: +#line 322 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); + p--; {goto st702;} + } +#line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -14523,12 +14612,12 @@ case 707: case 457: case 458: case 459: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -14544,12 +14633,12 @@ case 707: case 172: case 173: case 174: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -14565,12 +14654,12 @@ case 707: case 203: case 204: case 205: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -14585,12 +14674,12 @@ case 707: case 271: case 272: case 273: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14609,16 +14698,42 @@ case 707: case 366: case 367: case 368: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + break; + case 481: + case 482: + case 483: + case 484: + case 485: + case 486: + case 487: + case 488: + case 489: + case 490: +#line 322 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); + p--; {goto st702;} + } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -14631,12 +14746,12 @@ case 707: case 384: case 385: case 386: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14652,12 +14767,12 @@ case 707: case 466: case 479: case 480: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} @@ -14673,12 +14788,12 @@ case 707: case 181: case 199: case 200: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -14694,12 +14809,12 @@ case 707: case 212: case 268: case 269: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -14715,12 +14830,12 @@ case 707: case 280: case 359: case 360: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14741,12 +14856,12 @@ case 707: case 378: case 379: case 380: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} @@ -14761,12 +14876,12 @@ case 707: case 392: case 437: case 438: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14779,7 +14894,7 @@ case 707: break; case 147: case 148: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} @@ -14797,12 +14912,12 @@ case 707: break; case 196: case 197: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} @@ -14815,12 +14930,12 @@ case 707: break; case 251: case 252: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -14832,12 +14947,12 @@ case 707: } break; case 319: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14864,16 +14979,39 @@ case 707: case 429: case 430: case 431: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + break; + case 447: + case 448: + case 449: + case 450: + case 451: + case 452: + case 453: +#line 337 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); + p--; {goto st702;} + } +#line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -14888,16 +15026,40 @@ case 707: case 476: case 477: case 478: -#line 325 "vcf_v41.ragel" +#line 337 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); p--; {goto st702;} } -#line 234 "vcf_v41.ragel" +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } +#line 40 "vcf_v41.ragel" + { + ErrorPolicy::handle_meta_section_error(*this); + p--; {goto st702;} + } + break; + case 492: + case 493: + case 494: + case 495: + case 496: + case 497: + case 498: + case 499: +#line 337 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Metadata URL is not valid"); + p--; {goto st702;} + } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -14928,17 +15090,17 @@ case 707: break; case 321: case 331: -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -14950,17 +15112,17 @@ case 707: } break; case 404: -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14972,17 +15134,17 @@ case 707: } break; case 415: -#line 304 "vcf_v41.ragel" +#line 316 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Mixture contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -14994,17 +15156,17 @@ case 707: } break; case 169: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} @@ -15016,17 +15178,17 @@ case 707: } break; case 393: -#line 315 "vcf_v41.ragel" +#line 327 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata ID contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 299 "vcf_v41.ragel" +#line 311 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "SAMPLE metadata Genomes contains a character different from alphanumeric, dot, underscore and dash"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} @@ -15038,22 +15200,22 @@ case 707: } break; case 320: -#line 320 "vcf_v41.ragel" +#line 332 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Metadata description string is not valid"); p--; {goto st702;} } -#line 277 "vcf_v41.ragel" +#line 283 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Source string is not valid"); p--; {goto st702;} } -#line 282 "vcf_v41.ragel" +#line 288 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "INFO metadata Version string is not valid"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} @@ -15065,7 +15227,7 @@ case 707: } break; case 18: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -15075,36 +15237,46 @@ case 707: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -15113,7 +15285,7 @@ case 707: break; case 17: case 20: -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -15123,36 +15295,46 @@ case 707: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -15170,7 +15352,7 @@ case 707: ErrorPolicy::handle_fileformat_section_error(*this); p--; {goto st702;} } -#line 310 "vcf_v41.ragel" +#line 322 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in metadata"); p--; {goto st702;} @@ -15180,36 +15362,46 @@ case 707: ErrorPolicy::handle_fileformat_section_error(*this, "Error in ALT metadata"); p--; {goto st702;} } -#line 240 "vcf_v41.ragel" +#line 246 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FILTER metadata"); p--; {goto st702;} } -#line 246 "vcf_v41.ragel" +#line 252 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in FORMAT metadata"); p--; {goto st702;} } -#line 262 "vcf_v41.ragel" +#line 268 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in INFO metadata"); p--; {goto st702;} } #line 234 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in assembly metadata"); + p--; {goto st702;} + } +#line 240 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in contig metadata"); p--; {goto st702;} } -#line 294 "vcf_v41.ragel" +#line 306 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in SAMPLE metadata"); p--; {goto st702;} } -#line 288 "vcf_v41.ragel" +#line 294 "vcf_v41.ragel" { ErrorPolicy::handle_fileformat_section_error(*this, "Error in PEDIGREE metadata"); p--; {goto st702;} } +#line 300 "vcf_v41.ragel" + { + ErrorPolicy::handle_fileformat_section_error(*this, "Error in pedigreeDB metadata"); + p--; {goto st702;} + } #line 40 "vcf_v41.ragel" { ErrorPolicy::handle_meta_section_error(*this); @@ -15221,14 +15413,14 @@ case 707: p--; {goto st703;} } break; -#line 15225 "vcf_validator_detail.hpp" +#line 15417 "vcf_validator_detail.hpp" } } _out: {} } -#line 629 "vcf_v41.ragel" +#line 641 "vcf_v41.ragel" }