Variants.py -

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class Variants.Variant(pos, reference, genotype)

Bases: tuple

Create new instance of Variant(pos, reference, genotype)

property genotype

Alias for field number 2

property pos

Alias for field number 0

property reference

Alias for field number 1

Variants.ExtendedVariant

alias of Variants.Variant

Variants.updateVariants(variants, lcontig, strand, phased=True)

update variants such that they use same coordinate system (and strand) as the transcript

fixes 1-ness of variants

Variants.mergeVariants(variants)

merge overlapping variants.

Overlapping variants occur if there are two deletions at the same location:

WT ACTG Allele1 -CT- Allele2 —-

This will be encoded by samtools as (0-based coordinates):

0 * -A/ACTG
3 * -G/-G

This upsets the re-constitution algoritm.

This method separates these two variants into two non-overlapping variants making use of variable length deletions.

0 * -A/-A 1 * —G/-CTG

Another case:

WT ACTG Allele1 ACT- Allele2 —-

This will be encoded by samtools as (0-based coordinates):

0 * */-ACTG
3 * -G/*

This method separates these two as:

0 * */-ACT
3 * -G/-G

Variants.indexVariants(variants)

build index of variants for ranged retrieval.

Variants.buildAlleles(sequence, variants, reference_start=0, phased=True)

build alleles for sequence adding variants.

Variants are assumed to be in 0-based coordinates on the same strand as the sequence. reference_start is the position of the first base of sequence. Set to 0, if the positions in variants are relative to sequence.

Variants.buildOffsets(variants, phased=True, contig=None)

collect coordinate offsets.

This methods takes a set of variants and computes coordinates offsets based on indels.

Conflicting variants will be removed.

Returns a list of variants, a list of removed variants and a list of offsets.