ReadFilter
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', filter: { flagExclude: 1540, properPairs: 'exclude', split: 'only' } }{ type: 'LinearAlignmentsDisplay', filter: { tagFilters: [{ tag: 'HP', value: '1' }] } }See the Config slots section below for all available configuration fields.
Every read filter of the alignments display in one object, its filter
slot: the SAM flag masks, a read name, the tag filters a read has to pass
every one of, and the four read categories, each only, exclude or
unset for unfiltered. The default excludes unmapped, QC-failed and duplicate
reads (flag 1540).
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.
| Slot | Description |
|---|---|
flagIncludenumber = defaultFilterFlags.flagInclude | a read passes only with every one of these SAM flag bits set, samtools -f |
flagExcludenumber = defaultFilterFlags.flagExclude | a read passes only with none of these SAM flag bits set, samtools -F; 1540 drops unmapped, QC-failed and duplicate reads |
readNamemaybeString | the one read name shown; unset shows every read |
| tagFilters TagFilter | The tags a read has to carry, every one of them: a { tag, value } each, the value * or unset passing any read with the tag. |
splicedmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: reads whose CIGAR carries a reference skip. |
properPairsmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: pairs the aligner flagged proper, in normal orientation. |
singletonsmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: reads whose mate and supplementary segments are all outside the window. |
splitmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: reads with a supplementary segment, a chimeric alignment. |