MafAlignments
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the maf plugin. View source.
The MAF display's alignments setting: the per-species rows, the band that
takes the height the bands above it leave, and the layers drawn over the
fill encoding.color gives them. Letters keep the case the file gives
them, lowercase being soft-masked repeat in a UCSC alignment.
Example usage
{ type: 'LinearMafDisplay', alignments: { inversions: { show: true } } }Config slots
A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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.
| Slot | Description |
|---|---|
showboolean = true | When off, only the bands above the rows render. |
| mark MafAlignmentsMark | The glyph each base draws as: height.band, the fraction of its row it fills. |
| mismatches MafMismatches | show draws each base differing from the reference, with insertion markers and deletion counts; on by default. |
| bases MafBases | The per-position layer: every base, or each codon's amino-acid change. |
| inversions MafPart | show hatches each block a species aligns on the other strand from the rest of its blocks on that source chromosome. |
| frames MafPart | show draws each species' CDS reading frames from the MAF adapter's framesAdapter (UCSC mafFrames) as a strip over its row; no effect without one. |
| reference MafReferenceRow | show gives the reference species, which every other row is scored against, a row of its own; on by default. |