AlignmentsSort

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the alignments plugin. View source.

Example usage#

{ type: 'LinearAlignmentsDisplay', sort: 'spliced' }

{
  type: 'LinearAlignmentsDisplay',
  sort: { type: 'tag', tag: 'HP', pos: 1999, refName: 'ctgA' },
}

The alignments displays' sort setting: the pileup's row order. A whole-window order is a string — "position" (by start, the default), "length" (widest first), "spliced" (reads whose CIGAR carries a skip first), "split" (reads aligned in pieces first) or "svSignal" (split reads and reads carrying a deletion of 50 bp or more first, the evidence for a structural variant). A column sort ranks the reads over one base, pos (0-based) on refName, by strand, basePair, mapq (highest first), pairOrientation (the abnormal orientations over LR), tag (naming tag), or the insertion, softclip or hardclip there, or up to within bases either side; the reads not over it lay out by position. On another chromosome a column sort orders by position.

Related links#

• Extended by: LGVSyntenySort

Config slots#

Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.