Automation, Refactoring, and Mismap Fixes

[koisland]

• Changed count_complete_cens rule to count complete centromeres after accounting for partial centromeres.
  • Fixes #16
• Bumped arr_len_thr params in calculate_HOR_length.py to prevent including small HOR arrays.
  • Fixes #14
• Added edge-case fixes for specific chromsomes in calculate_HOR_length.py.
• Fixed bug in calculate_HOR_length.py with incorrect length difference calculation.
• Added missing chrY RepeatMasker reference annotations.
  • Fixes #15
• Refactored centromere identification workflow to align to the reference centromeres and filter alignments that include the monomeric regions on the p and q arms of the centromere.
  • Fixes #18
• Automated NucFreq misassembly detection with NucFreq fork.
• Fixed version of minimap2 v2.26 as v2.27 omits MD tag in SAM header causing failure in piping to samtools view.
• Refactored outputs to reduce output directory clutter.
• Refactored multiple awk commands to avoid using sed-split inputs which can fail with different ID formats.
• Moved centromere status checker script to a separate repo.
• Refactored renaming step to rename assembly fasta instead of repeatedly renaming fasta files and generating ID legends.