cljam.io.bcf.reader
meta-infoclj
(meta-info rdr)Returns meta-information of the BCF from rdr as a map.
Returns meta-information of the BCF from rdr as a map.
read-variantsclj
(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 a 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.
Returns data lines of the BCF from rdr as a lazy sequence of maps. rdr must implement cljam.bcf.BCFReader. Can take a 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.
readerclj
(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.
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.
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