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    • Logic

      • The field values are generated from quickLoadUrl + "/" + genome_name + "/annots.xml".
      • Consider only <file> tags where reference="none".
      • This URL returns the following fields: track, bigDataUrl, shortLabel, longLabel, type, and visibility.
        1. track – The first word in the title attribute.
        2. bigDataUrl – The name field of the <file> tag if it is already a URL. Otherwise, it is constructed as quickLoadUrl + "/" + genome_name + "/" + name.
        3. shortLabel – The last word of the title attribute.
        4. longLabel – The description field of the <file> tag.
        5. type – Determined based on the file extension of bigDataUrl.
          1. genomic_extensions = {
                        'bigWig': ['bw', 'bigwig'],
                        'bigBed 12': ['bb', 'bigbed'],
                        'bigGenePred': ['bb'],
                        'bigChain': ['bigchain'],
                        'bigNarrowPeak': ['bb'],
                        'bigBarChart': ['bb'],
                        'bigInteract': ['bb'],
                        'bigPsl': ['bb'],
                        'bigMaf': ['bb'],
                        'hic': ['hic'],
                        'bam': ['bam', 'cram'],
                        'HAL': ['hal'],
                        'vcfTabix': ['vcf', 'vcf.gz']
                    }
          2. Get the extension of bigDataUrl.
          3. If the extension is present in genomic_extensions and equals "bb", check whether the word before .bb matches a key in genomic_extensions. If yes, return that key (e.g., bigGenePred).
          4. Example: GSE63189_Catalog_of_lncRNAs_in_MCF-7cells.bigGenePred.bb → bigGenePred
          5. Otherwise, if the extension matches a value in genomic_extensions, return the corresponding key.
          6. If the extension is just .bb, return bigBed 12.
        6. visibility – Always set to "dense".

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