Changes

We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele).  The orange representation is not left aligned while the blue representation is.

We define an indel to be left aligned when the variant can not be shifted to the left any further while ensuring that the indel represented is consistent and that no alleles are represented with an empty string (empty allele).  The orange representation is not left aligned while the blue representation is.

== How to observe that a variant is not left aligned? ==

=== How to observe that a variant is not left aligned? ===

If the ends of each allele is the same nucleotide, it is not left aligned.

If the ends of each allele is the same nucleotide, it is not left aligned.

== Proof of left alignment ==

=== Proof of left alignment ===

Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).

Suppose an indel is already left aligned. In order to shift the variant to the right, we have to be able to truncate the first leftmost nucleotide in each allele without any loss of information (i.e. we can reconstruct the original alleles from the right aligned version of the variant given the reference genome). In order to guarantee this, the first leftmost nucleotide in each allele should be the same type of nucleotide (in other words, the same as the reference nucleotide).