API.md

Existence stat

/stat
params:
- reference_name (string)
- start_position (int64)
- end_position (int64)
- reference_bases (string of [ACTG]+)
- alternate_bases (string of [ACTG]+)
- position_range (boolean, default=true)

/stat_by_gene/{gene_name}
params: {same as /stat}
path_params:
- gene_name (string, must be a known gene name in UCSC GoldenPath dataset)

Variant counting

/count

Variant data query

/variants
params: {same as /stat}

/variants_by_gene/{gene_name}
params: {same as /variants}
path_params: {same as /stat_by_gene/{gene_name}}

Annotation data query

The assumption is that a variant table already exists, either as a permanent table or as the result of a variant query from /variants.

The 

Response Format

If data_count is zero, then keys "headers" and "data" may or may not exist

{
    "swarm_database_type": "athena|bigquery",
    "swarm_database_name": "swarm",
    "swarm_database_table": "genome_query_<random-value>",
    "data_count": 2, 
    "headers": [
        "reference_name",
        "start_position",
        "end_position",
        "reference_bases",
        "alternate_bases",
        "minor_af",
        "allele_count"],
    "data": [
        ["1", 1000, 1001, "A", "T", 0.005, 10],
        ["1", 1010, 1012, "AA", "AT", 0.005, 10]
    ]
}