cljam.algo.sorter
Sorter of the SAM/BAM format alignments.
default-chunk-size
Default number of alignments to split when sorting.
merge-sorted-seqs-by
(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!
(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
(sort-by-pos rdr wtr & [option])
Sorts alignments by chromosomal position.
sort-by-qname
(sort-by-qname rdr wtr & [option])
Sort alignments by query name.
sort-order
(sort-order rdr)
Returns sorting order of the sam as Keyword. Returning order is one of the
following: :queryname, :coordinate, :unsorted, :unknown.
sorted?
(sorted? rdr)
Returns true if the sam is sorted, false if not. It is detected by
`@HD SO:***` tag in the header.