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: { svSignal: 'only' } }{ type: 'LinearAlignmentsDisplay', filter: { minMapq: 20 } }{ type: 'LinearAlignmentsDisplay', filter: { tagFilters: [{ tag: 'HP', value: '1' }] } }Every read filter of the alignments display in one object, its filter
slot: the SAM flag masks, a minimum mapping quality, 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 |
minMapqmaybeNumber | a read passes only with a mapping quality of at least this; a read whose mapping quality is unavailable (255) fails it. Unset passes every read |
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. |
svSignalmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: reads carrying SV evidence, and the rest of their pair in the same displayed region. A read is evidence when it is split, carries an insertion or deletion of 50 bp or more, or is a paired primary read the aligner did not call concordant (no 0x2, a mate unmapped or on another chromosome, or a pair not facing FR). Both ends must be placed: a read at MAPQ 0 carries no evidence, a split read counts only when some other piece in its SA tag has MAPQ above 0, and a discordant read only when its mate does, where the MQ tag records it. |
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. |