/
Common.cpp
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/
Common.cpp
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//
// Expansion Hunter
// Copyright (c) 2016 Illumina, Inc.
//
// Author: Egor Dolzhenko <edolzhenko@illumina.com>,
// Mitch Bekritsky <mbekritsky@illumina.com>, Richard Shaw
// Concept: Michael Eberle <meberle@illumina.com>
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
//
#include "common/Common.hh"
using std::string;
namespace ehunter
{
Sex decodeSampleSex(const std::string& encoding)
{
if (encoding == "male")
{
return Sex::kMale;
}
else if (encoding == "female")
{
return Sex::kFemale;
}
else
{
throw std::invalid_argument(encoding + " is invalid sex; must be either male or female");
}
}
std::ostream& operator<<(std::ostream& out, ReadType readType)
{
switch (readType)
{
case ReadType::kFlanking:
out << "FLANKING";
break;
case ReadType::kRepeat:
out << "INREPEAT";
break;
case ReadType::kSpanning:
out << "SPANNING";
break;
case ReadType::kOther:
out << "OTHER";
}
return out;
}
std::ostream& operator<<(std::ostream& out, AlleleCount alleleCount)
{
switch (alleleCount)
{
case AlleleCount::kZero:
out << "Zero alleles";
break;
case AlleleCount::kOne:
out << "One allele";
break;
case AlleleCount::kTwo:
out << "Two alleles";
}
return out;
}
std::ostream& operator<<(std::ostream& out, NumericInterval numericInterval)
{
out << numericInterval.start() << "-" << numericInterval.end();
return out;
}
}