4. BGEN format

version 1.2

def filetype binary;
def endianness little;

[1]<uint32; :offset_to_first>(name="offset to the first data block")
[1]<uint32; :header_size>(name="header size in byte")
[1]<uint32; :variants_num>(name="number of variants")
[1]<uint32; :sample_num>(name="number of samples")
[4]<char; =['b', 'g', 'e', 'n']>(name="magic number")
[header_size - 20]<byte>(name="conserved bytes")

#flags
[2]<bit>(name="compression flat"; choices={0, 1}; id="compression")
[4]<bit>(name="layout type"; id="layout_type"; choices={0, 1, 2})
[25]<bit>(name="not defined bits")
[1]<bit; :sample_data>(name="indication for whether including sample indentifier data"; choices={0, 1}; id="sample_data")

if (sample_data) {
    [1]<uint32>(name="size of sample data block in byte")
    [1]<uint32; :sample_num_2>(name="sample name")
    assert sample_num == sample_num_2;
    [sample_num] {
        [1]<uint16; :indentifier_len>(name="length of indentifier of one sample")
        [indentifier_len]<char>(name="indentifier")(encode=ascii)
    }
}

[variants_num]{
    [1]<uint32>
    [1]<uint16; :vari_id_len>(name="length of variant identifier")
    [vari_id_len]<char>(name="the variant identifier"; encode=ascii)
    [1]<uint16; :rsid_len>(name="characteristic lenght of rsid")
    [rsid_len]<char>(name="rsid"; encode=ascii)
    [1]<uint16; :len_chrom> (name="lenght of chromosome string")
    [len_chrom]<char>(name="chromosome"; encode="ascii")
    [1]<uint32>(name="the variant position")
    [1]<uint16; :allel_num>(name="number of allels")
    [allel_num] {
        [1]<uint32; :allel_len>(name="length of allel string")
        [allel_len]<char>(name="the allel string", encode=ascii)
    }
}

if (layout == 1) {
    if (compression == 1) {
        [1]<uint32; compressed_data_len>(name="size of compressed genotype data")
        [compressed_data_len]<byte>(name="compressed data, uing zlib compressed")
    }
    if (compression == 0) {
        [variants_num * 6]<byte>(name="variants_num")
    }
}

if (layout == 2) {
    [1]<uint32; data_size>(name="the offset to the next variant block or end of file")
        if (compress_flg == 1) {
            [1]<uint32; :decompressed_size>(name="size after decompress")
            [data_size - 4]<byte; :vair_data_compressed>(name="compressed data")
        }
        if (compression == 0) {
            [data_size]<byte; :vair_data_ori>(name="data which not compressed")
        }
}