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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Tests for the paramChooser.h header.
//
// Currently, we only test the I/O routines from this file.
// ==========================================================================
#undef SEQAN_ENABLE_TESTING
#define SEQAN_ENABLE_TESTING 1
#include <sstream>
#include <seqan/basic.h>
#include <seqan/file.h>
#include "../splazers/paramChooser.h"
SEQAN_DEFINE_TEST(test_param_chooser_quality_distribution_from_prb_file)
{
seqan2::ParamChooserOptions pmOptions;
pmOptions.totalN = 4; // Read length.
pmOptions.verbose = false;
pmOptions.qualityCutoff = 10; // Ignore reads with smaller average quality than threshold.
seqan2::String<double> qualDist;
std::stringstream ss;
ss << "40 -40 -40 -40 10 20 30 40 30 30 20 10 10 20 10 10\n"
<< "10 -40 -40 -40 10 10 0 10 9 0 0 0 5 5 5 10\n"
<< "40 -40 -40 -40 10 20 30 40 30 30 20 10 10 20 10 10";
ss.seekg(0);
qualityDistributionFromPrbFile(ss, qualDist, pmOptions);
SEQAN_ASSERT_EQ(length(qualDist), 4u);
SEQAN_ASSERT_IN_DELTA(qualDist[0], 9.999e-05, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[1], 9.999e-05, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[2], 0.000999001, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[3], 0.00990099, 1.0e-07);
}
SEQAN_DEFINE_TEST(test_param_chooser_quality_distribution_from_fastq_file)
{
seqan2::ParamChooserOptions pmOptions;
pmOptions.totalN = 4; // Read length.
pmOptions.verbose = false;
pmOptions.qualityCutoff = 10; // Ignore reads with smaller average quality than threshold.
seqan2::String<double> qualDist;
std::stringstream ss;
ss << "@1\n"
<< "CGAT\n"
<< "+\n"
<< "II?5\n"
// << "@2\n" // see prb test, but from FASTQ does not kick out bad reads
// << "CGAT\n"
// << "+\n"
// << "+!*+\n"
<< "@3\n"
<< "CGAT\n"
<< "+\n"
<< "II?5";
ss.seekg(0);
qualityDistributionFromFastQFile(ss, qualDist, pmOptions);
SEQAN_ASSERT_EQ(length(qualDist), 4u);
SEQAN_ASSERT_IN_DELTA(qualDist[0], 9.999e-05, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[1], 9.999e-05, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[2], 0.000999001, 1.0e-07);
SEQAN_ASSERT_IN_DELTA(qualDist[3], 0.00990099, 1.0e-07);
}
SEQAN_DEFINE_TEST(test_param_chooser_parse_gapped_params)
{
seqan2::ParamChooserOptions pmOptions;
pmOptions.totalN = 4; // Read length.
pmOptions.verbose = false;
pmOptions.chooseOneGappedOnly = false;
pmOptions.chooseUngappedOnly = false;
pmOptions.minThreshold = 3;
pmOptions.optionLossRate = 0.01;
seqan2::RazerSOptions<> rOptions;
std::stringstream ss;
ss << "errors shape t lossrate PM\n"
<< "\n"
<< "0 11000000100100101 3 0 40895\n"
<< "1 11000000100100101 2 0 492286\n"
<< "2 11000000100100101 1 0.0293446 48417798\n"
<< "3 11000000100100101 1 0.195237 48417798\n"
<< "0 1111100001 10 0 40484\n"
<< "1 1111100001 7 0.163535 48622\n"
<< "1 1111100001 6 0.0497708 51290\n"
<< "1 1111100001 5 0 61068\n"
<< "1 1111101 4 0 61068";
ss.seekg(0);
SEQAN_ASSERT(parseGappedParams(rOptions, ss, pmOptions));
SEQAN_ASSERT_EQ(rOptions.shape, "1111100001");
SEQAN_ASSERT_EQ(rOptions.threshold, 10);
pmOptions.chooseOneGappedOnly = true;
ss.clear();
ss.seekg(0);
SEQAN_ASSERT(parseGappedParams(rOptions, ss, pmOptions));
SEQAN_ASSERT_EQ(rOptions.shape, "1111100001");
SEQAN_ASSERT_EQ(rOptions.threshold, 10);
pmOptions.chooseUngappedOnly = true;
ss.clear();
ss.seekg(0);
SEQAN_ASSERT_NOT(parseGappedParams(rOptions, ss, pmOptions));
}
SEQAN_DEFINE_TEST(test_param_parse_shapes_from_file)
{
seqan2::ParamChooserOptions pmOptions;
std::stringstream ss;
ss << " 11000000100100101 \n"
<< "1111100001\n"
<< "1111100001";
ss.seekg(0);
seqan2::String<seqan2::CharString> shapes;
SEQAN_ASSERT_EQ(parseShapesFromFile(shapes, ss, pmOptions), 3);
SEQAN_ASSERT_EQ(length(shapes), 3u);
SEQAN_ASSERT_EQ(shapes[0], "11000000100100101");
SEQAN_ASSERT_EQ(shapes[1], "1111100001");
SEQAN_ASSERT_EQ(shapes[2], "1111100001");
}
SEQAN_BEGIN_TESTSUITE(test_param_chooser)
{
SEQAN_CALL_TEST(test_param_chooser_quality_distribution_from_prb_file);
SEQAN_CALL_TEST(test_param_chooser_quality_distribution_from_fastq_file);
SEQAN_CALL_TEST(test_param_chooser_parse_gapped_params);
SEQAN_CALL_TEST(test_param_parse_shapes_from_file);
}
SEQAN_END_TESTSUITE
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