cljam.io.vcf.util — cljam 0.6.1-SNAPSHOT

dot-or-nil? clj

(dot-or-nil? s)

Checks if given string is equal to "." or nil.

genotype->ints clj

(genotype->ints gt)

Convert genotype to a sequence of integers.

info-parser clj

(info-parser info-meta)

Returns a parser function defined by meta-info. info-meta must be a sequence of map containing keys :id, :number and :type. The parser takes a string and returns a map.

info-stringifier clj

(info-stringifier info-meta)

Returns a stringifier function of INFO field. Takes a vector of maps from info rows of meta-info. The stringifier takes a map and returns a string.

ints->genotype clj

(ints->genotype vs)

Convert a sequence of integers to genotype string.

parse-filter clj

(parse-filter s)

Parses FILTER field and returns a sequence of keywords.

parse-format clj

(parse-format s)

Parses FORMAT field and returns as a sequence of keywords.

parse-genotype clj

(parse-genotype gt)

Parses genotype (GT) format and returns a vector of pairs: [allele, phased]. Allele 0 indicates REF allele. 1,2,3... for 1st, 2nd, 3rd allele of ALT.

sample-parser clj

(sample-parser formats-meta)

Returns a parser function defined by meta-formats. info must be a sequence of map containing keys :id, :number and :type. The parser takes two string (format-line and sample-line) and returns a map.

stringify-filter clj

(stringify-filter fltr)

Stringifies FILTER field. Takes a sequence of keywords or strings.

stringify-format clj

(stringify-format formats)

Stringifies FORMAT field. Takes a sequence of keywords or strings.

stringify-genotype clj

(stringify-genotype gt-seq)

Stringifies genotype map into VCF-style GT string.

stringify-sample clj

(stringify-sample formats sample-map)

Converts sample map into string. formats must be a seqeunce of keys in sample-map.

variant-parser clj

(variant-parser meta-info header)

Returns a parser function to parse :filter, :info, :FORMAT and sample columns of VCF. Takes meta-info and header of VCF. The parser takes a variant map and returns a parsed map.

variant-vals-stringifier clj

(variant-vals-stringifier meta-info header)

Returns a stringifier function to stringify :filter, :info, :FORMAT and sample columns of VCF. Takes meta-info and header of VCF. The stringifier takes a parsed variant map and returns a map.