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wfa_lm_st.hpp
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wfa_lm_st.hpp
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//
// wfa_lm_st.hpp
//
// MIT License
//
// Copyright (c) 2022 Jordan Eizenga
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in all
// copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
#ifndef wfa_lm_st_hpp_included
#define wfa_lm_st_hpp_included
#include "wfa_lm.hpp"
#include <sdsl/construct.hpp>
#include <sdsl/cst_sada.hpp>
#include <sdsl/cst_sct3.hpp>
#include <sdsl/csa_bitcompressed.hpp>
namespace wfalm {
/*
* Class that performs WFA with the standard, low-memory, or recusive variants.
* This class differs from WFAligner in that it uses a longest-common-extension
* algorithm based on a suffix tree to compute matches. In most cases, this is
* slower than the default comparison-based match computation.
*/
template<int NumPW>
class WFAlignerST : public WFAligner<NumPW> {
public:
/// Initialize with WFA-style score parameters. On opening an insertion or
/// deletion, *both* the gap open and gap extend penalties are applied.
/// Scores returned by alignment methods will also be WFA-style.
WFAlignerST(uint32_t mismatch,
std::array<uint32_t, std::max(1, NumPW)> gap_extend,
std::array<uint32_t, NumPW> gap_open);
/// Initialize with Smith-Waterman-Gotoh-style score parameters. On opening an
/// insertion or deletion, *both* the gap open and gap extend penalties are applied.
/// Scores returned by alignment methods will also be Smith-Waterman-Gotoh-style.
WFAlignerST(uint32_t match, uint32_t mismatch,
std::array<uint32_t, std::max(1, NumPW)> gap_extend,
std::array<uint32_t, NumPW> gap_open);
/// Default constructor. Performs edit distance alignment.
WFAlignerST();
/*****************************
* Configurable parameters *
*****************************/
/// If set to a number >= 0, prunes diagonals that fall this many anti-diagonals
/// behind the furthest-reaching diagonal. This can lead to suboptimal alignments,
/// but it also can increase speed and reduce memory use. If set to a number < 0,
/// no pruning is performed.
using WFAligner<NumPW>::lagging_diagonal_prune;
/***********************
* Alignment methods *
***********************/
/// Globally align two sequences using the fastest algorithm that will remain
/// constrained to a given maximum memory, using a suffix tree to compute matches
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
/// target_mem The target maximum memory use in bytes
///
/// Return value:
/// Pair consisting of CIGAR string for alignment and the alignment score.
inline std::pair<std::vector<CIGAROp>, int32_t>
wavefront_align_adaptive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
uint64_t max_mem) const;
/// Globally align two sequences in O(s log s) memory using the recursive WFA algorithm,
/// using a suffix tree to compute matches.
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
///
/// Return value:
/// Pair consisting of CIGAR string for alignment and the alignment score.
inline std::pair<std::vector<CIGAROp>, int32_t>
wavefront_align_recursive(const char* seq1, size_t len1,
const char* seq2, size_t len2) const;
/// Globally align two sequences in O(s^3/2) memory using the low-memory WFA algorithm,
/// using a suffix tree to compute matches.
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
///
/// Return value:
/// Pair consisting of CIGAR string for alignment and the alignment score.
inline std::pair<std::vector<CIGAROp>, int32_t>
wavefront_align_low_mem(const char* seq1, size_t len1,
const char* seq2, size_t len2) const;
/// Globally align two sequences in O(s^2) memory using the standard WFA algorithm,
/// using a suffix tree to compute matches.
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
///
/// Return value:
/// Pair consisting of CIGAR string for alignment and the alignment score.
inline std::pair<std::vector<CIGAROp>, int32_t>
wavefront_align(const char* seq1, size_t len1,
const char* seq2, size_t len2) const;
/// Locally align two sequences from a seed using the adaptive WFA as an
/// alignment engine. *Can only called if WFAligner was initialized with
/// Smith-Waterman-Gotoh scoring parameters in the constructor.*
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
/// max_mem The target maximum memory use in bytes
/// anchor_begin_1 First index of the anchor on seq1
/// anchor_end_1 Past-the-last index of the anchor on seq1
/// anchor_begin_2 First index of the anchor on seq2
/// anchor_end_2 Past-the-last index of the anchor on seq2
/// anchor_is_match If false, the anchor sequence will be aligned, otherwise
/// it will be assumed to be a match
///
/// Return value:
/// A tuple consisting of:
/// - CIGAR string for alignment
/// - the alignment score
/// - a pair of indexes indicating the interval of aligned sequence on seq1
/// - a pair of indexes indicating the interval of aligned sequence on seq2
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
wavefront_align_local_adaptive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
uint64_t max_mem,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match = true) const;
/// Locally align two sequences from a seed using the recursive WFA as an
/// alignment engine. *Can only called if WFAligner was initialized with
/// Smith-Waterman-Gotoh scoring parameters in the constructor.*
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
/// anchor_begin_1 First index of the anchor on seq1
/// anchor_end_1 Past-the-last index of the anchor on seq1
/// anchor_begin_2 First index of the anchor on seq2
/// anchor_end_2 Past-the-last index of the anchor on seq2
/// anchor_is_match If false, the anchor sequence will be aligned, otherwise
/// it will be assumed to be a match
///
/// Return value:
/// A tuple consisting of:
/// - CIGAR string for alignment
/// - the alignment score
/// - a pair of indexes indicating the interval of aligned sequence on seq1
/// - a pair of indexes indicating the interval of aligned sequence on seq2
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
wavefront_align_local_recursive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match = true) const;
/// Locally align two sequences from a seed using the low memory WFA as an
/// alignment engine. *Can only called if WFAligner was initialized with
/// Smith-Waterman-Gotoh scoring parameters in the constructor.*
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
/// anchor_begin_1 First index of the anchor on seq1
/// anchor_end_1 Past-the-last index of the anchor on seq1
/// anchor_begin_2 First index of the anchor on seq2
/// anchor_end_2 Past-the-last index of the anchor on seq2
/// anchor_is_match If false, the anchor sequence will be aligned, otherwise
/// it will be assumed to be a match
///
/// Return value:
/// A tuple consisting of:
/// - CIGAR string for alignment
/// - the alignment score
/// - a pair of indexes indicating the interval of aligned sequence on seq1
/// - a pair of indexes indicating the interval of aligned sequence on seq2
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
wavefront_align_local_low_mem(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match = true) const;
/// Locally align two sequences from a seed using the standard WFA as an
/// alignment engine. *Can only called if WFAligner was initialized with
/// Smith-Waterman-Gotoh scoring parameters in the constructor.*
///
/// Args:
/// seq1 First sequence to be aligned (need not be null-terminated)
/// len1 Length of first sequence to be aligned
/// seq2 Second sequence to be aligned (need not be null-terminated)
/// len2 Length of second sequence to be aligned
/// anchor_begin_1 First index of the anchor on seq1
/// anchor_end_1 Past-the-last index of the anchor on seq1
/// anchor_begin_2 First index of the anchor on seq2
/// anchor_end_2 Past-the-last index of the anchor on seq2
/// anchor_is_match If false, the anchor sequence will be aligned, otherwise
/// it will be assumed to be a match
///
/// Return value:
/// A tuple consisting of:
/// - CIGAR string for alignment
/// - the alignment score
/// - a pair of indexes indicating the interval of aligned sequence on seq1
/// - a pair of indexes indicating the interval of aligned sequence on seq2
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
wavefront_align_local(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match = true) const;
};
/*******************************************************************
*******************************************************************
*** Only internal methods below here ***
*******************************************************************
*******************************************************************/
typedef sdsl::cst_sada<sdsl::csa_bitcompressed<>,
sdsl::lcp_dac<1>,
sdsl::bp_support_gg<sdsl::nearest_neighbour_dictionary<1>,
sdsl::rank_support_v<>,
sdsl::select_support_mcl<>, 64>,
sdsl::rank_support_v<10, 2>,
sdsl::select_support_mcl<10, 2>> SuffixTree;
// a match computing function based on the suffix tree
struct STMatchFunc {
public:
STMatchFunc() = default;
~STMatchFunc() = default;
protected:
template<typename StringType>
void init(const StringType& seq1, const StringType& seq2) {
offset = seq1.size() + 1;
// encoding:
// a/A 1
// c/C 2
// g/G 3
// t/T 4
// else 5
// $ 6
static const uint8_t separator = 6;
static const uint8_t st_encode[256] {
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 0
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 32
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(1), uint8_t(5), uint8_t(2), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(3),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 64
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(4), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(1), uint8_t(5), uint8_t(2), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(3),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 96
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(4), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 128
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 160
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 192
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), //
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), // 224
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5),
uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5), uint8_t(5) //
};
// TODO: i wish this were possible with an implicit copy, but looks like probably not
// since the sdsl::store_to_file that backends the in-memory construction is only
// specialized for string and char*
// - but also this gets us around the StringView vs. string issues in local alignment...
// encode the joined string and the sentinel in a 3-bit alphabet
std::string combined_seq(seq1.size() + seq2.size() + 1, 0);
size_t i;
for (i = 0; i < seq1.size(); ++i) {
combined_seq[i] = st_encode[seq1[i]];
}
combined_seq[i] = separator;
++i;
for (size_t j = 0; j < seq2.size(); ++i, ++j) {
combined_seq[i] = st_encode[seq2[j]];
}
// construct in memory with 1-byte words
sdsl::construct_im(suffix_tree, combined_seq, 1);
}
inline size_t lce(size_t i, size_t j) const {
// in sdsl, suffix array indexes are 0-based, but leaf ranks are 1-based
return suffix_tree.depth(suffix_tree.lca(suffix_tree.select_leaf(suffix_tree.csa.isa[i] + 1),
suffix_tree.select_leaf(suffix_tree.csa.isa[offset + j] + 1)));
}
SuffixTree suffix_tree;
size_t offset;
};
class FwdSTMatchFunc : STMatchFunc {
public:
FwdSTMatchFunc(const StringView& seq1, const StringView& seq2) {
init<StringView>(seq1, seq2);
}
inline size_t operator()(size_t i, size_t j) const {
return lce(i, j);
}
};
class RevSTMatchFunc : STMatchFunc {
public:
RevSTMatchFunc(const RevStringView& seq1, const RevStringView& seq2) {
init<RevStringView>(seq1, seq2);
}
inline size_t operator()(size_t i, size_t j) const {
return lce(i, j);
}
};
template<int NumPW>
WFAlignerST<NumPW>::WFAlignerST() : WFAligner<NumPW>() {}
template<int NumPW>
WFAlignerST<NumPW>::WFAlignerST(uint32_t mismatch,
std::array<uint32_t, std::max(1, NumPW)> gap_extend,
std::array<uint32_t, NumPW> gap_open)
: WFAligner<NumPW>(mismatch, gap_extend, gap_open)
{
// only need to delegate to WFAligner
}
template<int NumPW>
WFAlignerST<NumPW>::WFAlignerST(uint32_t match, uint32_t mismatch,
std::array<uint32_t, std::max(1, NumPW)> gap_extend,
std::array<uint32_t, NumPW> gap_open)
: WFAligner<NumPW>(match, mismatch, gap_extend, gap_open)
{
// only need to delegate to WFAligner
}
template<int NumPW>
inline std::pair<std::vector<CIGAROp>, int32_t>
WFAlignerST<NumPW>::wavefront_align(const char* seq1, size_t len1,
const char* seq2, size_t len2) const {
StringView str1(seq1, 0, len1);
StringView str2(seq2, 0, len2);
return WFAligner<NumPW>::template wavefront_dispatch<false, WFAligner<NumPW>::StdMem, FwdSTMatchFunc>(str1, str2,
std::numeric_limits<uint64_t>::max());
}
template<int NumPW>
inline std::pair<std::vector<CIGAROp>, int32_t>
WFAlignerST<NumPW>::wavefront_align_low_mem(const char* seq1, size_t len1,
const char* seq2, size_t len2) const {
StringView str1(seq1, 0, len1);
StringView str2(seq2, 0, len2);
return WFAligner<NumPW>::template wavefront_dispatch<false, WFAligner<NumPW>::LowMem, FwdSTMatchFunc>(str1, str2,
std::numeric_limits<uint64_t>::max());
}
template<int NumPW>
inline std::pair<std::vector<CIGAROp>, int32_t>
WFAlignerST<NumPW>::wavefront_align_recursive(const char* seq1, size_t len1,
const char* seq2, size_t len2) const {
StringView str1(seq1, 0, len1);
StringView str2(seq2, 0, len2);
return WFAligner<NumPW>::template wavefront_dispatch<false, WFAligner<NumPW>::Recursive, FwdSTMatchFunc>(str1, str2,
std::numeric_limits<uint64_t>::max());
}
template<int NumPW>
inline std::pair<std::vector<CIGAROp>, int32_t>
WFAlignerST<NumPW>::wavefront_align_adaptive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
uint64_t max_mem) const {
StringView str1(seq1, 0, len1);
StringView str2(seq2, 0, len2);
return WFAligner<NumPW>::template wavefront_dispatch<false, WFAligner<NumPW>::AdaptiveMem, FwdSTMatchFunc>(str1, str2, max_mem);
}
template<int NumPW>
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
WFAlignerST<NumPW>::wavefront_align_local(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match) const {
// configure the alignment and match functions
typedef typename WFAligner<NumPW>::template StandardSemilocalWFA<RevSTMatchFunc, RevStringView> PrefWFA;
typedef typename WFAligner<NumPW>::template StandardGlobalWFA<FwdSTMatchFunc, StringView> AnchorWFA;
typedef typename WFAligner<NumPW>::template StandardSemilocalWFA<FwdSTMatchFunc, StringView> SuffWFA;
return WFAligner<NumPW>::template wavefront_align_local_core<PrefWFA, AnchorWFA, SuffWFA>(seq1, len1, seq2, len2,
std::numeric_limits<uint64_t>::max(),
anchor_begin_1, anchor_end_1,
anchor_begin_2, anchor_end_2,
anchor_is_match);
}
template<int NumPW>
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
WFAlignerST<NumPW>::wavefront_align_local_low_mem(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match) const {
// configure the alignment and match functions
typedef typename WFAligner<NumPW>::template LowMemSemilocalWFA<RevSTMatchFunc, RevStringView> PrefWFA;
typedef typename WFAligner<NumPW>::template LowMemGlobalWFA<FwdSTMatchFunc, StringView> AnchorWFA;
typedef typename WFAligner<NumPW>::template LowMemSemilocalWFA<FwdSTMatchFunc, StringView> SuffWFA;
return WFAligner<NumPW>::template wavefront_align_local_core<PrefWFA, AnchorWFA, SuffWFA>(seq1, len1, seq2, len2,
std::numeric_limits<uint64_t>::max(),
anchor_begin_1, anchor_end_1,
anchor_begin_2, anchor_end_2,
anchor_is_match);
}
template<int NumPW>
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
WFAlignerST<NumPW>::wavefront_align_local_recursive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match) const {
// configure the alignment and match functions
typedef typename WFAligner<NumPW>::template RecursiveSemilocalWFA<RevSTMatchFunc, RevStringView> PrefWFA;
typedef typename WFAligner<NumPW>::template RecursiveGlobalWFA<FwdSTMatchFunc, StringView> AnchorWFA;
typedef typename WFAligner<NumPW>::template RecursiveSemilocalWFA<FwdSTMatchFunc, StringView> SuffWFA;
return WFAligner<NumPW>::template wavefront_align_local_core<PrefWFA, AnchorWFA, SuffWFA>(seq1, len1, seq2, len2,
std::numeric_limits<uint64_t>::max(),
anchor_begin_1, anchor_end_1,
anchor_begin_2, anchor_end_2,
anchor_is_match);
}
template<int NumPW>
inline std::tuple<std::vector<CIGAROp>, int32_t, std::pair<size_t, size_t>, std::pair<size_t, size_t>>
WFAlignerST<NumPW>::wavefront_align_local_adaptive(const char* seq1, size_t len1,
const char* seq2, size_t len2,
uint64_t max_mem,
size_t anchor_begin_1, size_t anchor_end_1,
size_t anchor_begin_2, size_t anchor_end_2,
bool anchor_is_match) const {
// configure the alignment and match functions
typedef typename WFAligner<NumPW>::template AdaptiveSemilocalWFA<RevSTMatchFunc, RevStringView> PrefWFA;
typedef typename WFAligner<NumPW>::template AdaptiveGlobalWFA<FwdSTMatchFunc, StringView> AnchorWFA;
typedef typename WFAligner<NumPW>::template AdaptiveSemilocalWFA<FwdSTMatchFunc, StringView> SuffWFA;
return WFAligner<NumPW>::template wavefront_align_local_core<PrefWFA, AnchorWFA, SuffWFA>(seq1, len1, seq2, len2, max_mem,
anchor_begin_1, anchor_end_1,
anchor_begin_2, anchor_end_2,
anchor_is_match);
}
} // end namespace wfalm
#endif /* wfa_lm_st.hpp */