cljam.io.vcf.util — cljam 0.8.0

biallelic-coll clj

(biallelic-coll ploidy n-alt-alleles target-allele coll)

Picks up elements in multiallelic coll and make a biallelic one. Ignores all alleles other than the reference allele and the target-allele.

biallelic-genotype clj

(biallelic-genotype genotype target-allele)

Converts a multiallelic genotype string into a biallelic one. Ignores all alleles other than the reference allele and the target-allele.

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.

genotype-index clj

(genotype-index genotype)

Returns an index for given genotype.

genotype-seq clj

(genotype-seq ploidy n-alt-alleles)

(genotype-seq ploidy n-alt-alleles s)

Returns a sequence of genotypes represented as sequences 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.

inspect-allele clj

(inspect-allele ref alt)

Inspects an alt allele by comparing to a ref allele string. Returns a map containing :type and other detailed information. A value of the key :type can be one of the followings:

• :no-call No variant called
• :spanning-deletion Placeholder to signify an absent sequence
• :unspecified Unspecified non-ref allele
• :ref Duplicated allele of REF
• :id Symbolic reference
• :snv Single nucleotide variant
• :mnv Multiple nucleotide variants
• :insertion Insertion of a short base sequence
• :deletion Deletion of a short base sequence
• :complete-insertion Complete insertion of a long sequence
• :breakend Breakend of a complex rearrangement
• :complex Complex nucleotide variants other than snv/mnv/indel
• :other Can't categorize the allele, might be malformed

ints->genotype clj

(ints->genotype vs)

Convert a sequence of integers to genotype string.

parse-breakend clj

(parse-breakend alt)

Parses an ALT allele string of SVTYPE=BND. Returns a map with mandatory keys:

• :bases bases that replaces the reference place
• :join :before or :after and optional keys for a mate:
• :chr chromosome name of the mate sequence
• :pos genomic position of the mate sequence
• :strand strand of the mate sequence Returns nil if input alt is not a breakend.

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-breakend clj

(stringify-breakend {:keys [chr pos strand join] s :bases})

Returns a string representation of a breakend. If the input is malformed, returns nil. See the docstring of parse-breakend for the format.

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 sequence 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.