Module translate

Translating deterministic k-bounded matching statistics into alignments.

The translated alignment is encoded using the following characters:

• M : Match between query and reference.
• - : Characters in the query that are not found in the reference.
• X : Single character mismatch or insertion into the query.
• I : Single or multiple base insertion into the query.
• D : Deletion in the query.
• R : Two consecutive ’R’s signify a discontinuity in the alignment. The right ‘R’ is at the start of a k-mer that is not adjacent to the last character in the k-mer corresponding to the left ‘R’. This implies either a deletion of unknown length in the query, or insertion of k-mers from elsewhere in the reference into the query.

‘I’ and ‘D’ are only used if add_variants was called.

Functions

add_variants

Add variant calling results to a translated alignment.

translate_ms_val

Translates a single derandomized k-bounded matching statistic.

translate_ms_vec

Translates a sequence of derandomized k-bounded matching statistics.