Panclade alignment

[aineniamh]

• Adding in pan clade composite consensus reference generated from an alignment of PX667572 and NC_063383.
• The gene boundaries file for pan clade contains genes from clade I and clade II with coordinates mapped from the original reference sequence to the pan clade coordinate system
• The ITR is trimmed from 193610, which is the ITR mask site for clade II mapped onto the new coordinate system
• The mask file is currently empty
• Some translation functions are included that can generate the coordinate system map (in utils/panclade_map.py). To access the coordinate map run the following:

import squirrel.utils.panclade_map as pm
coordinates = pm.get_coordinate_map()

• This function extracts coordinate mappings from predefined CIGAR strings.
  Retrieves a dictionary of CIGAR strings for reference sequences and
  converts each CIGAR string into bidirectional coordinate mappings
  between genomic and alignment positions.
  Returns:
  dict: Dictionary mapping sequence IDs to coordinate information dictionaries,
  each containing:
  - cigar (str): CIGAR string representation.
  - genome_to_aln (dict): Maps genome positions to alignment positions.
  - aln_to_genome (dict): Maps alignment positions to genome positions,
  with None for gap positions.