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// ==========================================================================
// Yara - Yet Another Read Aligner
// ==========================================================================
// Copyright (c) 2011-2026, Enrico Siragusa, 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 Enrico Siragusa 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 ENRICO SIRAGUSA 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: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
#ifndef APP_YARA_MAPPER_CLASSIFIER_H_
#define APP_YARA_MAPPER_CLASSIFIER_H_
using namespace seqan2;
// ============================================================================
// Classes
// ============================================================================
// ----------------------------------------------------------------------------
// Class ReadsClassifier
// ----------------------------------------------------------------------------
// One instance per thread.
template <typename TSpec, typename TConfig>
struct ReadsClassifier
{
typedef typename TConfig::TReadsContext TReadsContext;
typedef typename TConfig::THits THits;
typedef typename TConfig::TSeeds TSeeds;
typedef typename TConfig::TReadSeqs TReadSeqs;
// Shared-memory read-write data.
TReadsContext & ctx;
THits & hits;
// Shared-memory read-only data.
TSeeds const & seeds;
TReadSeqs const & readSeqs;
Options const & options;
ReadsClassifier(TReadsContext & ctx,
THits & hits,
TSeeds const & seeds,
Options const & options) :
ctx(ctx),
hits(hits),
seeds(seeds),
readSeqs(host(seeds)),
options(options)
{
_classifyReadsImpl(*this);
}
template <typename TReadSeqsIterator>
void operator() (TReadSeqsIterator const & it)
{
_classifyReadImpl(*this, it);
}
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _classifyReadsImpl()
// ----------------------------------------------------------------------------
template <typename TSpec, typename TConfig>
inline void _classifyReadsImpl(ReadsClassifier<TSpec, TConfig> & me)
{
typedef typename TConfig::TReadSeqs TReadSeqs;
typedef Segment<TReadSeqs const, PrefixSegment> TPrefix;
TPrefix pairs(me.readSeqs, getReadsCount(me.readSeqs));
// Iterate over all pairs.
iterate(pairs, me, Rooted(), typename TConfig::TThreading());
}
// ----------------------------------------------------------------------------
// Function _classifyReadImpl()
// ----------------------------------------------------------------------------
template <typename TSpec, typename TConfig, typename TReadSeqsIterator>
inline void _classifyReadImpl(ReadsClassifier<TSpec, TConfig> & me, TReadSeqsIterator const & it)
{
typedef typename TConfig::THits THits;
typedef typename Value<THits>::Type THit;
typedef typename Id<THit>::Type THitId;
typedef Pair<THitId> THitIds;
typedef typename Size<THit>::Type THitSize;
typedef typename TConfig::TSeeds TSeeds;
typedef typename Id<TSeeds>::Type TSeedId;
typedef Pair<TSeedId> TSeedIds;
typedef typename TConfig::TReadSeqs TReadSeqs;
typedef typename Size<TReadSeqs>::Type TReadId;
// Get readSeqId.
TReadId fwdSeqId = position(it);
// Get mate id.
TReadId revSeqId = getFirstMateRevSeqId(me.readSeqs, fwdSeqId);
// Get seed ids.
TSeedIds fwdSeedIds = getSeedIds(me.seeds, fwdSeqId);
TSeedIds revSeedIds = getSeedIds(me.seeds, revSeqId);
// Get hit ids.
THitIds fwdHitIds = getHitIds(me.hits, fwdSeedIds);
THitIds revHitIds = getHitIds(me.hits, revSeedIds);
// Count the hits of each read.
THitSize fwdHits = countHits<THitSize>(me.hits, fwdHitIds);
THitSize revHits = countHits<THitSize>(me.hits, revHitIds);
THitSize readHits = fwdHits + revHits;
// Re-seed hard reads.
if (readHits > me.options.hitsThreshold)
{
// Guess a good seeding stragegy.
unsigned seedErrors = (readHits < 2 * 200 * me.options.hitsThreshold) ? 1 : 2;
setSeedErrors(me.ctx, fwdSeqId, seedErrors);
setSeedErrors(me.ctx, revSeqId, seedErrors);
// Clear the hits of the read.
clearHits(me.hits, fwdHitIds);
clearHits(me.hits, revHitIds);
}
}
#endif // #ifndef APP_YARA_MAPPER_CLASSIFIER_H_
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