A library for working with phylogenetic and population genetic data.
v0.27.0
simple_pileup_common.hpp
Go to the documentation of this file.
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#ifndef GENESIS_POPULATION_FORMATS_SIMPLE_PILEUP_COMMON_H_
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#define GENESIS_POPULATION_FORMATS_SIMPLE_PILEUP_COMMON_H_
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/*
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Genesis - A toolkit for working with phylogenetic data.
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Copyright (C) 2014-2022 Lucas Czech
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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Contact:
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Lucas Czech <lczech@carnegiescience.edu>
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Department of Plant Biology, Carnegie Institution For Science
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260 Panama Street, Stanford, CA 94305, USA
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*/
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#include "
genesis/population/formats/simple_pileup_reader.hpp
"
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#include <string>
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#include <vector>
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namespace
genesis
{
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namespace
population {
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// =================================================================================================
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// Simple (m)pileup Reader Helper Functions
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// =================================================================================================
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BaseCounts
convert_to_base_counts
(
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SimplePileupReader::Sample
const
& sample,
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unsigned
char
min_phred_score = 0
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);
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Variant
convert_to_variant
(
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SimplePileupReader::Record
const
& record,
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unsigned
char
min_phred_score = 0
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);
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}
// namespace population
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}
// namespace genesis
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#endif // include guard
genesis::population::convert_to_variant
Variant convert_to_variant(SimplePileupReader::Record const &record, unsigned char min_phred_score)
Definition:
simple_pileup_common.cpp:145
genesis::population::convert_to_base_counts
BaseCounts convert_to_base_counts(SimplePileupReader::Sample const &sample, unsigned char min_phred_score)
Definition:
simple_pileup_common.cpp:45
simple_pileup_reader.hpp
genesis
Container namespace for all symbols of genesis in order to keep them separate when used as a library.
Definition:
placement/formats/edge_color.cpp:42
lib
genesis
population
formats
simple_pileup_common.hpp
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