cljam.io.vcf.reader — cljam 0.8.5

A type of VCF reader and internal functions to read VCF contents. See https://samtools.github.io/hts-specs/ for the detail VCF specifications.

load-header clj

(load-header rdr)

Reads from rdr and parses them as header.

load-meta-info clj

(load-meta-info rdr)

Reads from rdr and parses them as meta-info.

parse-header-line clj

(parse-header-line line)

Parses a single line string as header

parse-meta-info-line clj

(parse-meta-info-line line)

Parses a single line string as meta-info.

read-file-offsets clj

(read-file-offsets rdr)

Reads file offsets and a genomic position of variants from bgzip compressed VCF and returns them as a lazy sequence. Each element is a map containing :chr, :chr-index, :beg, :end, :file-beg, :file-end.

read-variants clj

(read-variants rdr)

(read-variants rdr {:keys [depth] :or {depth :deep}})

Reads variants of the VCF/BCF file, returning them as a lazy sequence.

read-variants-randomly clj

(read-variants-randomly rdr
                        {:keys [chr start end] :or {start 1 end 4294967296}}
                        {:keys [depth] :or {depth :deep}})

Reads variants of the bgzip compressed VCF file randomly using tabix/csi file Returning them as a lazy sequence.