Further information on r2d liftover

R2Dtool liftover enables the rapid conversion from coordinates mapped in transcriptomic space, to coordinates mapped in genomic space.

We provide pseudocode for the convert_transcriptomic_to_genomic_coordinates function that is invoked by the r2d liftover command:

Algorithm: convert_transcriptomic_to_genomic_coordinates

Inputs: 
  - site_fields: array of strings containing transcriptomic information
  - annotations: hashmap of transcript annotations
  - has_version: boolean indicating if transcript IDs include version numbers

Output: 
  - String containing genomic coordinates or None if conversion fails

1. If length of site_fields < 4:
    Return None

2. transcript_id_with_version ← site_fields[0]

3. If has_version:
    transcript_id ← transcript_id_with_version
   Else:
    transcript_id ← Split transcript_id_with_version by '.' and take first part

4. position ← Parse site_fields[1] as integer

5. current_position ← 0

6. If transcript_id exists in annotations:
    transcript ← annotations[transcript_id]
    
    7. Sort exons of transcript:
       If transcript.strand = '-':
           Sort exons in descending order by start position
       Else:
           Sort exons in ascending order by start position
    
    8. For each exon in sorted exons:
        exon_length ← exon.end - exon.start + 1
        
        9. If current_position + exon_length > position:
            If transcript.strand = '+':
                genomic_position ← position - current_position + exon.start - 1
            Else:
                genomic_position ← exon.end - (position - current_position) - 1
            
            10. chrom ← transcript.chromosome
                genomic_strand ← transcript.strand
                additional_columns ← Join site_fields[1:] with tab separator
            
            11. Return formatted string:
                "{chrom}\t{genomic_position}\t{genomic_position + 1}\t\t\t{genomic_strand}\t{transcript_id_with_version}\t{additional_columns}"
        
        12. current_position ← current_position + exon_length

13. Print warning: "No associated transcripts found for site '{transcript_id}'"
14. Return None

Original source code for the liftover function is available at https://github.com/comprna/R2Dtool/blob/main/src/liftover.rs