7.4. BGEN format

version 1.2

[1] <uint32; :$offset_to_data> (dsp="offset to first data block")

[1] <uint32; :$header_size> <dsp="size in byte of header block">
[1] <uint32; :$vari_num> <dsp="variant number">
[1] <uint32; :$sample_num> <dsp="sample number">
[4] <char; =["b", "g", "e", "n"]> (dsp="megic number")
[$header_size - 20] <byte> <dsp="free data area">

[1] {
    [2] <bit; ={0, 1}> (dsp="flag for whether compressed"; value="0 for not compressed, 1 for compressed")
    [4] <bit; ={0, 1, 2}> (dsp="layout"; value="0: layout 0; 1: layout 1; 2: layout 2")
    [25] <bit> (dsp="not defined")
    [1] <bit; :$sample_flg> (dsp="indicate whether include sample indentifier data"; value="0: not included; 1: included")

} (dsp="flags")


[%if $sample_flg] {
    [1] <uint32> (dsp="size in byte of sample indentifier block")
    [1] <uint32; :$sample_num_2> (dsp="number of sample")
    [%assert $sample_num_2 == $sample_num]
    [$sample_num] {
        [1] <uint16; :$indentifier_string_len> (dsp="length of indentifier of one sample")
        [$indentifier_string_len] <char> (dsp="indentifier")

    } (dsp="sample data, the data is char, should interpreted as ascii")

}


[$vari_num] {
    [1] <uint32> ()

    [1] <uint16; :$len_vari_id> (dsp="length of variant identifier")
    [$len_vari_id] <char> (dsp="the variant identifier"; type="ascii")
    [1] <uint16; :$len_rsid> (dsp="legth of rsid")
    [$len_rsid]<char> (dsp="rsid"; type="ascii")
    [1] <uint16; :$len_chrom> (dsp="lenght of chromosome string")
    [$len_chrom] <char> (dsp="chromosome"; type="ascii")
    [1] <uint32> (dsp="the variant position")
    [1] <uint16; :$allel_num> (dsp="number of allels")
    [$allel_num] {
        [1] <uint32; :$allel_len> (dsp="length of allel string")
        [$allel_len] <char> (dsp="the allel string"; type="ascii")

    }

    [%if $layout == 1] {
        [%if compress_flg == 1] {
            [1] <uint32; :$compressed_len> (dsp="size of compressed genotype data, if $compress_flg is 0, this segment is ignored")
            [$compressed_len] <byte; :@compressed_dt> (dsp="genotype data which is compressed")
            [%let @genotype_dt = $zlib_decompress(@compressed_dt)]
            [%assert $arraylen(@genotype_dt) == 6 * $vari_num]
        }

        [%elif $compress_flg == 0] {
            [$vari_num * 6] <byte; :@genotype_dt> (dsp="genotype data")
        }

        [%parse @genotype_dt] {

            [$sample_num] {
                [1] <uint16; :$pb1> (dsp="probability of homozygous of allel 1")
                [1] <uint16; :$pb2> (dsp="probability of Heterozygous")
                [1] <uint16; :$pb3> (dsp="probability of homozygous of allel 2")
            }

            [%let $pb1_converted = $convert_to_prob($pb1)]
            [%let $pb2_converted = $convert_to_prob($pb2)]
            [%let $pb2_converted = $convert_to_prob($pb3)]

        }
    }

    [%if $layout == 2] {
        [1] <uint32; $data_size> (dsp="the offset to the next variant block or end of file")

        [%if $compress_flg == 1] {
            [1] <uint32; :$decompressed_size> (dsp="size after decompress")
            [$data_size - 4] <byte; :@vair_data_compressed> (dsp="compressed data")
            [%let @vari_data_ori = $decompress_fuction(@vair_data_compressed)]
        }

        [%else] {
            [$data_size] <byte; :@vair_data_ori> (dsp="data which not compressed")
        }


        [%parse @vari_data_ori] {

            [1] <uint32> (dsp="number of individual")
            [1] <uint16> (dsp="number of allels")
            [1] <char> (dsp="minimum ploidy")
            [1] <char> (dsp="maximum ploidy")
            [$sample_num] <char> (dsp="ploidy of samples"; NA="most significant bit is 1")
            [1] <char> (dsp="denoted Phased indicating what is stored in the row")
            [1] <uint8> (dsp="number of bits used to store each probability in this row")
            [$?] <byte> ()
            //not finished yet

        }



    }

}

[%deffunc $convert_to_prob ($datain) $dataout] {
    [$dataout = $datain / 32768]
    [%return $dataout]

} (dsp="fuction to convert 16 bits integer into a float to get probability")

[%deffunc $convert_prob_to_int ($datain) $dataout] {

    [$dataout = $floor($datain * 32768)]

} (dsp="convert probability into a 16 bits integer")