Skip to main content

AlignmentsFilter

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

Every test the alignments display applies, in one object, its filter slot, read by every part that draws the data a test names: the base filter's read members and connections, and junctions, which tests the splice junctions.

Example usage

{
  type: 'LinearAlignmentsDisplay',
  filter: { junctions: { minReads: 5, nonCanonical: 'exclude' } },
}

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
junctions
JunctionFilter		The splice junctions drawn: minReads (default 2) and nonCanonical.
Inherited from BaseAlignmentsFilter10 slots
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).