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93 lines
2.8 KiB
93 lines
2.8 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.genotype;
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import bio.core.base;
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import bio.core.tinymap;
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/// Holds ordered pair of two alleles
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struct DiploidGenotype(B) {
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mixin TinyMapInterface!(B.ValueSetSize ^^ 2);
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private static ubyte _getCode(B b1, B b2) {
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auto c1 = b1.internal_code;
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auto c2 = b2.internal_code;
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return cast(ubyte)(c1 * B.ValueSetSize + c2);
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}
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/// Construct a genotype from two bases
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/// Every ambiguous base gets converted to 'N' internally.
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this(B b1, B b2) {
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_code = _getCode(b1, b2);
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}
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/// Construct homozygous genotype
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this(B b) {
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_code = _getCode(b, b);
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}
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/// First allele
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B base1() @property const {
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return B.fromInternalCode(_code / B.ValueSetSize);
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}
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/// Second allele
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B base2() @property const {
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return B.fromInternalCode(_code % B.ValueSetSize);
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}
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///
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bool is_heterozygous() @property const {
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return base1 != base2;
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}
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///
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bool is_homozygous() @property const {
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return base1 == base2;
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}
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/// String representation B1|B2 (TODO: add phasing in future?)
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string toString() const {
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return base1 ~ "|" ~ base2;
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}
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}
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/// Create an instance of DiploidGenotype
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auto diploidGenotype(B...)(B bases) {
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return DiploidGenotype!(B[0])(bases);
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}
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unittest {
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auto g1 = diploidGenotype(Base('C'), Base('W'));
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assert(g1.base1 == 'C');
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assert(g1.base2 == 'W');
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// By default, Base5 is used
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auto g2 = diploidGenotype(Base5('C'));
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assert(g2.base1 == g2.base2);
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// Both bases must be of the same type
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static assert(!__traits(compiles, diploidGenotype(Base5('T'), Base16('D'))));
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}
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