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update RLE normalization algo
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ahwagner committed Feb 19, 2024
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12 changes: 4 additions & 8 deletions docs/source/impl-guide/normalization.rst
Original file line number Diff line number Diff line change
Expand Up @@ -91,8 +91,8 @@ the following normalization rules apply:
and `Alternate Allele Sequence`.

#. one is empty, the input Allele is an insertion (empty `reference
sequence`) or a deletion (empty `alternate sequence`). Continue to
step 3.
sequence`) or a deletion (empty `alternate sequence`). The length of the
non-empty sequence is the `repeat subunit length`. Continue to step 3.

#. Determine bounds of ambiguity.

Expand All @@ -115,13 +115,9 @@ the following normalization rules apply:
Return a new `Allele` with the trimmed `Alternate Allele Sequence` as a `Literal
Sequence Expression`.

#. Otherwise, find the greatest common denominator between the length of the expanded `Reference
Allele Sequence` and the expanded `Alternate Allele Sequence`. This is the `repeat subunit length`.

#. If the Allele is a deletion (the `Alternate Allele Sequence` is shorter than the
`Reference Allele Sequence`) return a new Allele using a `Location` specified by the coordinates
#. If the Allele is a deletion, return a new Allele using a `Location` specified by the coordinates
of the `left_roll_bound` and `right_roll_bound`, a `length` specified by the length of the
`Alternate Allele Sequence`, and a `repeat subunit length` as calculated in the prior step.
expanded `Alternate Allele Sequence`, and a `repeat subunit length` as previously calculated.

#. If the Allele is an insertion (the `Reference Allele Sequence` is shorter than the
`Alternate Allele Sequence`), check that the first `repeat subunit length` number of characters
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