3. BOD file

Oii file

Stored individual information.

def filetype plaintext;
def encode ascii;
export line_num;
export oii_order;

[+:line_num]{
    [1]<string>(name="family ID")
    [1]<string>(name="individual ID")
    [1]<string>(name="patertal ID")
    [1]<string>(name="maternal ID")
    [1]<string>(name="sex"; datatype=int; NA="0";
                choices={"1", "2", "0"}; id="sex")
}(element_end="\n"; element_sub_sep="\t"; order=oii_order)

[# Notes
    sex: 1 for male; 2 for female; 0 for unknown.
]

Opi file

Storded probe information.

def filetype plaintext;
def encode ascii;
export line_num;
export opi_order;

[+:line_num]{
    [1]<string>(name="chromosome ID/name")
    [1]<string>(name="probe ID")
    [1]<string>(name="physical position")
    [1]<string>(name="gene ID")
    [1]<string>(name="gene orientation")
}(element_end="\n"; element_sub_sep="\t"; order=opi_order)

Bod file

def filetype binary;
def endianness little;
import oii_format;
import opi_format;

[1]<char>(name="value type"; choices={0, 1, 2}; id="value_type")
[1]<char>(name="data type"; choices={0, 1, 2}; id="data_type")
[2]<char; =0>(name="reserved bytes")
[1]<uint32; :indi_num>(name="number of individuals")
[2]<uint32; :probe_num>(name="numer of probes")
assert indi_num == oii_format.line_num;
assert probe_num == opi_format.line_num;
[probe_num]{
    [indi_num]<double>(align_with=oii_format.oii_order)
}(align_with=opi_format.opi_order)