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