cljam.io.bam.decoder — cljam 0.8.3

Decoder of BAM alignment blocks.

BAMPointerBlock clj

BAMRawBlock clj

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)

decode-options clj

(decode-options rest)

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)

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)

options-size clj

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

parse-tag-single clj

(parse-tag-single tag-type bb)

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)