cljam.io.bam.decoder — cljam 0.8.5

Decoder of BAM alignment blocks.

decode-alignment clj

(decode-alignment refs block)

(decode-alignment refs block start end)

Decodes BAM block and creates SAMAlignment instance which is compatible with SAM. When called with start and end, this function may return nil if any base of the block is not included in the range.

decode-coordinate-block clj

(decode-coordinate-block block)

(decode-coordinate-block block start end)

Decodes BAM block and returns a SAMCoordinateBlock instance containing ref-id, pos and flag.

decode-next-ref-id clj

(decode-next-ref-id refs ref-id next-ref-id)

Returns "=" if ref and next is same reference, otherwise returns next-ref-name.

decode-options clj

(decode-options rest')

Decodes bytes of bam options.

decode-pointer-block clj

(decode-pointer-block block)

(decode-pointer-block block start end)

Decodes BAM block and returns a BAMPointerBlock instance containing region, flag and block pointers.

decode-qual clj

(decode-qual b)

Decodes qual from bytes. Returns "*" if input is filled with 0xff, otherwise returns qual.

decode-queryname-block clj

(decode-queryname-block block)

(decode-queryname-block block start end)

Decodes BAM block and returns a SAMQuerynameBlock instance containing qname and flag.

decode-region-block clj

(decode-region-block block)

(decode-region-block block start end)

Decodes BAM block and returns a SAMRegionBlock instance containing covering range of the alignment.

decode-seq clj

(decode-seq seq-bytes length)

Decodes seq from bytes. Returns "*" if seq is empty, otherwise returns sequence.

options-size clj

(options-size block-size l-read-name n-cigar-op l-seq)

Returns the number of bytes of the trailing optional fields.

parse-tag-single clj

(parse-tag-single tag-type bb)

Parses a tag according to tag-type.

raw-block clj

(raw-block b)

(raw-block b s e)

Checks the range of BAM block and returns the given block if any base is included.

validate-tag-type clj

(validate-tag-type t)

Changes (u)int8 or (u)int16 tag type to int32 tag type.