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BaseAlignmentsFilter

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

The filter both alignments-shaped displays read, LinearAlignmentsDisplay and LGVSyntenyDisplay. The read members are the SAM flag masks, a minimum mapping quality, a read name, the tags a read must have, and the four read categories, each only, exclude or unset for unfiltered; the default excludes unmapped, QC-failed and duplicate reads (flag 1540). connections tests the connections between mates and split segments. Every test must hold, so two categories both apply: { split: 'only', svSignal: 'only' } keeps the split reads alone.

Example usage

{ type: 'LinearAlignmentsDisplay', filter: { svSignal: 'only' } }
{ type: 'LinearAlignmentsDisplay', filter: { minMapq: 20 } }
{ type: 'LinearAlignmentsDisplay', filter: { tags: [{ tag: 'HP', value: '1' }] } }

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.

SlotDescription
flagInclude
number = 0		a read passes only with every one of these SAM flag bits set, samtools -f
flagExclude
number = 1540		a read passes only with none of these SAM flag bits set, samtools -F; 1540 drops unmapped, QC-failed and duplicate reads
minMapq
maybeNumber		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
readName
maybeString		the one read name shown; unset shows every read
tags
TagFilter		The tags a read must have, every one of them: a { tag, value } each, and an unset value matches any read with the tag.
spliced
maybeStringEnum (only, exclude)		only, exclude, or unset for unfiltered: reads whose CIGAR has a reference skip.
svSignal
maybeStringEnum (only, exclude)		only, exclude, or unset for unfiltered: reads with SV evidence, and the rest of their pair in the same displayed region. A read is evidence when it is split, has 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 is not 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, as the MQ tag records.
alone
maybeStringEnum (only, exclude)		only, exclude, or unset for unfiltered: reads with no other alignment of themselves in the window, no mate and no split or supplementary segment there. A mate unmapped, on another chromosome or outside the window counts, as does a single-end read with no SA tag.
split
maybeStringEnum (only, exclude)		only, exclude, or unset for unfiltered: reads with a supplementary segment, a chimeric alignment.
connections
ConnectionFilter		The connections drawn: interchrom, offscreenMates and minInterchromReads (default 2).