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#ifndef SHASTA_SEQAN_HPP
#define SHASTA_SEQAN_HPP
// Wrappers to simplify SeqAn calls.
// Shasta.
#include "SHASTA_ASSERT.hpp"
// Seqan.
#include <seqan/align.h>
// Standard library.
#include "utility.hpp"
#include "vector.hpp"
namespace shasta {
// Align two integer sequences using SeqAn and
// return the alignment score.
// The alignment is returned as a vector of pairs of bools,
// where false indicates a gap and true indicates a sequence element.
// For example, the following alignment
// ACTG-A
// A-TGTA
// would be returned as
// {true, true}, A,A
// {true, false} C,-
// {true, true}, T,T
// {true, true} G,G
// {false, true}, -,T
// {true, true} A,A
template<class Iterator>
int64_t seqanAlign(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
int64_t matchScore,
int64_t mismatchScore,
int64_t gapScore,
bool freeOnLeft,
bool freeOnRight,
vector< pair<bool, bool> >& alignment);
// Same, banded.
template<class Iterator>
int64_t seqanAlign(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
int64_t matchScore,
int64_t mismatchScore,
int64_t gapScore,
int64_t bandMin,
int64_t bandMax,
bool freeOnLeft,
bool freeOnRight,
vector< pair<bool, bool> >& alignment);
// Find out if the alignment computed by seqanAlign contains mismatches.
template<class Iterator>
bool containsMismatches(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
const vector< pair<bool, bool> >& alignment);
// Given an alignment computed by seqanAlign, find positions in the
// two sequences that contain aligned identical symbols.
template<class Iterator>
void findAlignedIdentical(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
const vector< pair<bool, bool> >& alignment,
vector< pair<uint64_t, uint64_t> >& alignedIdenticalPositions);
}
template<class Iterator>
int64_t shasta::seqanAlign(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
int64_t matchScore,
int64_t mismatchScore,
int64_t gapScore,
bool freeOnLeft,
bool freeOnRight,
vector< pair<bool, bool> >& alignment)
{
// SeqAn does not handle empty sequences.
SHASTA_ASSERT(begin0 != end0);
SHASTA_ASSERT(begin1 != end1);
// SeqAn types used below.
using namespace seqan2;
using Int = typename Iterator::value_type;
using Sequence = String<Int>;
using StringSet = seqan2::StringSet<Sequence>;
using DepStringSet = seqan2::StringSet<Sequence, Dependent<> >;
using AlignGraph = Graph<seqan2::Alignment<DepStringSet> >;
// Fill in the sequences, adding 100 to all values
// because SeqAn uses 45 to represent gaps.
Sequence sequence0;
for(Iterator it=begin0; it!=end0; it) {
appendValue(sequence0, *it 100);
}
Sequence sequence1;
for(Iterator it=begin1; it!=end1; it) {
appendValue(sequence1, *it 100);
}
// Store them in a SeqAn string set.
StringSet sequences;
appendValue(sequences, sequence0);
appendValue(sequences, sequence1);
// Compute the alignment.
// See https://docs.seqan.de/seqan/2.1.0/class_AlignConfig.html
// for meaning of AlignConfig.
AlignGraph graph(sequences);
int64_t alignmentScore = 0;
if(freeOnLeft) {
if(freeOnRight) {
// Free on both sides.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<true, true, true, true>(),
LinearGaps());
} else {
// Free on left only.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<true, true, false, false>(),
LinearGaps());
}
}else {
if(freeOnRight) {
// Free on right only.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<false, false, true, true>(),
LinearGaps());
} else {
// Free on neither side.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<false, false, false, false>(),
LinearGaps());
}
}
// Extract the alignment from the graph.
// This creates a single sequence consisting of the two rows
// of the alignment, concatenated.
Sequence align;
convertAlignment(graph, align);
const uint64_t totalAlignmentLength = seqan2::length(align);
SHASTA_ASSERT((totalAlignmentLength % 2) == 0);
const uint64_t alignmentLength = totalAlignmentLength / 2;
// Fill in the bool pairs representing the alignment.
alignment.resize(alignmentLength);
for(uint64_t i=0; i<alignmentLength; i ) {
auto& p = alignment[i];
p.first = not (align[i] == 45);
p.second = not (align[i alignmentLength] == 45);
}
return alignmentScore;
}
// Same, banded.
template<class Iterator>
int64_t shasta::seqanAlign(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
int64_t matchScore,
int64_t mismatchScore,
int64_t gapScore,
int64_t bandMin,
int64_t bandMax,
bool freeOnLeft,
bool freeOnRight,
vector< pair<bool, bool> >& alignment)
{
// SeqAn does not handle empty sequences.
SHASTA_ASSERT(begin0 != end0);
SHASTA_ASSERT(begin1 != end1);
// SeqAn types used below.
using namespace seqan2;
using Int = typename Iterator::value_type;
using Sequence = String<Int>;
using StringSet = seqan2::StringSet<Sequence>;
using DepStringSet = seqan2::StringSet<Sequence, Dependent<> >;
using AlignGraph = Graph<seqan2::Alignment<DepStringSet> >;
// Fill in the sequences, adding 100 to all values
// because SeqAn uses 45 to represent gaps.
Sequence sequence0;
for(Iterator it=begin0; it!=end0; it) {
appendValue(sequence0, *it 100);
}
Sequence sequence1;
for(Iterator it=begin1; it!=end1; it) {
appendValue(sequence1, *it 100);
}
// Store them in a SeqAn string set.
StringSet sequences;
appendValue(sequences, sequence0);
appendValue(sequences, sequence1);
// Compute the alignment.
// See https://docs.seqan.de/seqan/2.1.0/class_AlignConfig.html
// for meaning of AlignConfig.
AlignGraph graph(sequences);
int64_t alignmentScore = 0;
if(freeOnLeft) {
if(freeOnRight) {
// Free on both sides.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<true, true, true, true>(),
int32_t(bandMin), int32_t(bandMax),
LinearGaps());
} else {
// Free on left only.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<true, true, false, false>(),
int32_t(bandMin), int32_t(bandMax),
LinearGaps());
}
}else {
if(freeOnRight) {
// Free on right only.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<false, false, true, true>(),
int32_t(bandMin), int32_t(bandMax),
LinearGaps());
} else {
// Free on neither side.
alignmentScore = globalAlignment(
graph,
Score<int64_t, seqan2::Simple>(matchScore, mismatchScore, gapScore),
AlignConfig<false, false, false, false>(),
int32_t(bandMin), int32_t(bandMax),
LinearGaps());
}
}
// Extract the alignment from the graph.
// This creates a single sequence consisting of the two rows
// of the alignment, concatenated.
Sequence align;
convertAlignment(graph, align);
const uint64_t totalAlignmentLength = seqan2::length(align);
SHASTA_ASSERT((totalAlignmentLength % 2) == 0);
const uint64_t alignmentLength = totalAlignmentLength / 2;
// Fill in the bool pairs representing the alignment.
alignment.resize(alignmentLength);
for(uint64_t i=0; i<alignmentLength; i ) {
auto& p = alignment[i];
p.first = not (align[i] == 45);
p.second = not (align[i alignmentLength] == 45);
}
return alignmentScore;
}
// Find out if the alignment computed by seqanAlign contains mismatches.
template<class Iterator>
bool shasta::containsMismatches(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
const vector< pair<bool, bool> >& alignment)
{
Iterator it0 = begin0;
Iterator it1 = begin1;
for(const auto& p: alignment) {
if(p.first and p.second) {
if(*it0 != *it1) {
return true;
}
it0;
it1;
} else if(p.first) {
it0;
} else if(p.second) {
it1;
}
}
SHASTA_ASSERT(it0 == end0);
SHASTA_ASSERT(it1 == end1);
return false;
}
// Given an alignment computed by seqanAlign, find positions in the
// two sequences that contain aligned identical symbols.
template<class Iterator>
void shasta::findAlignedIdentical(
Iterator begin0, Iterator end0,
Iterator begin1, Iterator end1,
const vector< pair<bool, bool> >& alignment,
vector< pair<uint64_t, uint64_t> >& alignedIdenticalPositions)
{
alignedIdenticalPositions.clear();
Iterator it0 = begin0;
Iterator it1 = begin1;
uint64_t position0 = 0;
uint64_t position1 = 0;
for(const auto& p: alignment) {
if(p.first and p.second) {
if(*it0 == *it1) {
alignedIdenticalPositions.push_back(make_pair(position0, position1));
}
it0;
it1;
position0;
position1;
} else if(p.first) {
it0;
position0;
} else if(p.second) {
it1;
position1;
}
}
SHASTA_ASSERT(it0 == end0);
SHASTA_ASSERT(it1 == end1);
}
#endif
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