AlignmentsSort

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

The alignments displays' sort setting: the pileup's row order, by the field it ranks the reads on. A whole-window order is a string — "position" (by start, the default), "length" (widest first), "spliced" (reads whose CIGAR has a skip first), "split" (reads aligned in pieces first) or "svSignal" (the structural-variant evidence first, in tiers: split reads, then reads with an insertion or deletion of 50 bp or more, then paired reads the aligner did not call concordant, each with both ends placed above MAPQ 0, as the svSignal filter counts it). A column sort ranks the reads over one base, pos (0-based) on refName, by strand, base, mapq (highest first), pairOrientation (the abnormal orientations over LR), a SAM tag (tags.HP, spelt as encoding.color and facet spell one), 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.

Example usage#

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

{
  type: 'LinearAlignmentsDisplay',
  sort: { field: 'tags.HP', pos: 1999, refName: 'ctgA' },
}

Related links#

• Extended by: LGVSyntenySort

Config slots#

A setting written to it replaces it whole, since its members are alternatives: a member left out returns to its default. 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.