Module: BioVcf

Defined in:

lib/bio-vcf/vcfheader.rb,
lib/bio-vcf/vcf.rb,
lib/bio-vcf/utils.rb,
lib/bio-vcf/vcfrdf.rb,
lib/bio-vcf/variant.rb,
lib/bio-vcf/vcffile.rb,
lib/bio-vcf/vcfline.rb,
lib/bio-vcf/bedfilter.rb,
lib/bio-vcf/vcfrecord.rb,
lib/bio-vcf/vcfsample.rb,
lib/bio-vcf/vcfstatistics.rb,
lib/bio-vcf/vcfheader_line.rb,
lib/bio-vcf/vcfgenotypefield.rb

Overview

line 1 “gen_vcfheaderline_parser.rl” Ragel lexer for VCF-header

This is compact a parser/lexer for the VCF header format. Bio-vcf uses the parser to generate meta information that can be output to (for example) JSON format. The advantage of using ragel as a state engine is that it allows for easy parsing of key-value pairs with syntax checking and, for example, escaped quotes in quoted string values. This ragel parser/lexer generates valid Ruby; it should be fairly trivial to generate python/C/JAVA instead. Note that this edition validates ID and Number fields only. Other fields are dumped ‘AS IS’.

Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl

by Pjotr Prins © 2014/2015

Defined Under Namespace

Modules: ConvertStringToValue, RDF, Turtle, Variant, VcfHeaderParser, VcfLine, VcfRdf, VcfRecordCall, VcfRecordParser, VcfSample, VcfValue Classes: BedFilter, VCFfile, ValueError, VcfAltInfoList, VcfGenotypeField, VcfGenotypeFields, VcfHeader, VcfNucleotideCount4, VcfRecord, VcfRecordInfo, VcfStatistics

Constant Summary

MAXINT =

100_000