parsing csq header stuffs

scripts/csq.lua

@@ -65,10 +65,14 @@ function CSQ:__index(key)
     end
 end
 
+--[[
+
 header = { "Allele", "Consequence", "IMPACT", "cDNA_position", "AF" }
 vals = "A|missense_variant|MODERATE|c.1A>G|1.1e-05"
 
 c = CSQ.new(vals, header)
 print(tostring(c))
 print(c.Allele)
 print(c.AF)
+
+--]]

scripts/csq_header.lua

@@ -0,0 +1,60 @@
+function parse_description(description)
+    -- Remove quotes and spaces
+    description = description:gsub('"', ''):gsub('%s+', '')
+
+    -- Determine the correct split point
+    local format_str = nil
+    if description:find('Format:') then
+        format_str = description:match('Format:(.+)')
+    else
+        format_str = description:match(':\'(.+)')
+    end
+
+    if format_str then
+        -- Split by | delimiter and store in a table
+        local result = {}
+        for value in string.gmatch(format_str, '([^|]+)') do
+            -- Remove any trailing characters like ')' or ']'
+            value = value:gsub('[%)>\'%]%[]', '')
+            -- test if value startswith 'Effect(' and remove it if that's the case.
+            if value:find('Effect%(') then
+                value = value:gsub('^\'?Effect%(', '')
+            end
+
+            table.insert(result, value)
+        end
+        return result
+    else
+        return nil, "Format part not found in description."
+    end
+end
+
+--[[
+-- Example usage
+local input1 =
+'#INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE">'
+local input2 =
+'##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: \'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )\'">'
+local input3 =
+'##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: \'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO\'">'
+
+local parsed_table1 = parse_description(input1)
+local parsed_table2 = parse_description(input2)
+local parsed_table3 = parse_description(input3)
+
+print("Parsed Table 1:")
+for i, v in ipairs(parsed_table1) do
+    print(i, v)
+end
+
+print("\nParsed Table 2:")
+for i, v in ipairs(parsed_table2) do
+    print(i, v)
+end
+
+print("\nParsed Table 3:")
+for i, v in ipairs(parsed_table3) do
+    print(i, v)
+end
+
+--]]