Parser support

[dridk]

Create different kind of parser

• [x] Raw VCF
• [x] VEP
• [x] SnpEff
• [ ] Annovar
• [ ] Affymetrix
• [ ] MAF format
• [ ] Varank format

[dridk]

You must subclass AbstractReader class and override get_variants() and get_fields() @see FakeReader

get_fields() yield as follow :

    [
        {"name": "chr", "type": "text", "category": "variant", "description": "description"}
        
   ]

get_variant() yield as follow:

     [
       {"chr": "chr3",
       "pos": 3244,
       "ref": "A",
       "alt":"C", 
       "field_n": "value_n",
       "annotations": [ 
           {"gene": "GJB2", "transcripts": "NM_00232.1", "field_n": "value_n"},
           {"gene": "GJB2", "transcripts": "NM_00232.2", "field_n": "value_n"}
           ],
       "samples": [
           {"name":"boby", "gt": 1, "field_n":"value_n"},
           {"name":"kevin", "gt": 1, "field_n":"value_n"}
           ]}
    
       ]