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106 lines
3.0 KiB
106 lines
3.0 KiB
/*
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This file is part of BioD.
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Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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module bio.core.call;
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import bio.core.base;
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import bio.core.genotype;
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/// A genotype call
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struct Call(alias Gt, B)
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{
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alias Gt!B G;
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private {
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string _sample = void;
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string _chr = void;
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ulong _pos = void;
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B _refbase = void;
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G _gt = void;
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float _qual = void;
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}
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/// Constructor
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this(string sample, string chr, ulong pos,
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B refbase, G genotype, float quality=float.nan)
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{
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_sample = sample;
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_chr = chr;
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_pos = pos;
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_refbase = refbase;
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_gt = genotype;
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_qual = quality;
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}
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/// Sample name
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string sample() @property const {
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return _sample;
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}
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/// Chromosome name
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string chromosome() @property const {
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return _chr;
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}
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/// 0-based position on the reference
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ulong position() @property const {
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return _pos;
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}
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/// Reference base at the site
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B reference_base() @property const {
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return _refbase;
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}
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/// Most probable genotype
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ref const(G) genotype() @property const {
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return _gt;
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}
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///
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alias genotype this;
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/// Phred-scaled quality score. If unknown, set to NaN.
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float quality() @property const {
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return _qual;
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}
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/// Returns true if this call is not a reference one.
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bool is_variant() @property const {
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return _gt != G(_refbase);
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}
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}
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alias Call!(DiploidGenotype, Base5) DiploidCall5;
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alias Call!(DiploidGenotype, Base16) DiploidCall;
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alias DiploidCall DiploidCall16;
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unittest {
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auto call = DiploidCall("NA01234", "chr10", 543210,
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Base('T'), diploidGenotype(Base('C'), Base('T')),
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47.0);
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assert(call.is_variant);
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assert(call.is_heterozygous);
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assert(call.reference_base == 'T');
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}
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