cljam.algo.sorter — cljam 0.8.0

Sorter of the SAM/BAM format alignments.

default-chunk-size clj

merge-sorted-seqs-by clj

(merge-sorted-seqs-by key-fn seqs)

Returns a lazy sequence from pre-sorted sequences. Each sequences must be sorted by key-fn. Returns first sequence if only 1 sequence is given.

sort! clj

(sort! rdr wtr {:keys [mode chunk-size cache-fmt] :or {cache-fmt :bam}})

Sorts alignments of rdr by mode and writes them to wtr. :coordinate and :queryname are available for mode.

sort-by-pos clj

(sort-by-pos rdr wtr & [option])

Sorts alignments by chromosomal position.

sort-by-qname clj

(sort-by-qname rdr wtr & [option])

Sort alignments by query name.

sort-order clj

(sort-order rdr)

Returns sorting order of the sam as Keyword. Returning order is one of the following: :queryname, :coordinate, :unsorted, :unknown.

sorted? clj

(sorted? rdr)

Returns true if the sam is sorted, false if not. It is detected by @HD SO:*** tag in the header.