cljam.io.bcf.reader — cljam 0.8.3

meta-info clj

(meta-info rdr)

Returns meta-information of the BCF from rdr as a map.

read-file-offsets clj

(read-file-offsets rdr)

Reads file offsets and a genomic position of variants from BCF 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}})

Returns data lines of the BCF from rdr as a lazy sequence of maps. rdr must implement cljam.bcf.BCFReader. Can take an option :depth to specify parsing level. Default is :deep.

:deep Fully parsed variant map. FORMAT, FILTER, INFO and samples columns are parsed. :vcf VCF-style map. FORMAT, FILTER, INFO and samples columns are strings. :bcf BCF-style map. CHROM, FILTER, INFO and :genotype contains indices to meta-info. :shallow Only CHROM, POS and ref-length are parsed. :raw Raw map of ByteBufers.

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 BCF file randomly using csi file. Returns them as a lazy sequence.

reader clj

(reader f)

Returns an open cljam.bcf.reader.BCFReader of f. Should be used inside with-open to ensure the Reader is properly closed. Throws IOException if failed to parse BCF file format.