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Merged
eseiler merged 1 commit into from
Aug 12, 2025
Merged

First version alignment #3

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39 changes: 38 additions & 1 deletion include/fpgalign/search/search.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

#pragma once

#include <mutex>
#include <string>
#include <vector>

Expand All @@ -19,8 +20,44 @@ struct hit
std::vector<uint64_t> bins;
};

struct wip_alignment
{
size_t bin;
size_t sequence_number;
size_t position;
std::vector<uint8_t> seq;
std::vector<uint8_t> ref;
std::string id;
};

class alignment_vector
{
private:
std::vector<wip_alignment> data;
std::mutex mtx;

public:
std::vector<wip_alignment> & get() noexcept
{
return data;
}

std::vector<wip_alignment> const & get() const noexcept
{
return data;
}

void emplace_back(wip_alignment elem)
{
std::lock_guard guard{mtx};
data.emplace_back(std::move(elem));
}

void emplace_back(wip_alignment & elem) = delete;
};

void search(config const & config);
std::vector<hit> ibf(config const & config, size_t & todo_bin_count);
void fmindex(config const & config, std::vector<hit> hits, size_t const todo_bin_count);
std::vector<wip_alignment> fmindex(config const & config, std::vector<hit> hits, size_t const todo_bin_count);

} // namespace search
16 changes: 9 additions & 7 deletions src/argument_parsing.cpp
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Expand Up @@ -25,7 +25,8 @@ config parse_arguments(sharg::parser & parser)
.long_id = "output",
.description = "Output path",
.required = true,
.validator = sharg::output_file_validator{}}); // .ibf and .fmindex
.validator = sharg::output_file_validator{
sharg::output_file_open_options::open_or_create}}); // .ibf and .fmindex
parser.add_option(config.threads,
sharg::config{.short_id = '\0',
.long_id = "threads",
Expand Down Expand Up @@ -86,12 +87,13 @@ config parse_arguments(sharg::parser & parser)
.description = "Query path",
.required = true,
.validator = sharg::input_file_validator{}});
parser.add_option(config.output_path,
sharg::config{.short_id = '\0',
.long_id = "output",
.description = "Output path",
.required = true,
.validator = sharg::output_file_validator{}});
parser.add_option(
config.output_path,
sharg::config{.short_id = '\0',
.long_id = "output",
.description = "Output path",
.required = true,
.validator = sharg::output_file_validator{sharg::output_file_open_options::open_or_create}});
parser.add_option(config.threads,
sharg::config{.short_id = '\0',
.long_id = "threads",
Expand Down
4 changes: 2 additions & 2 deletions src/build/fmindex.cpp
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Expand Up @@ -34,7 +34,7 @@ std::vector<std::vector<uint8_t>> read_reference(std::vector<std::string> const
| std::views::transform(
[](auto const & in)
{
return seqan3::to_rank(in);
return seqan3::to_rank(in) + 1u;
}),
std::back_inserter(reference.back()));
}
Expand All @@ -48,7 +48,7 @@ void fmindex(config const & config)
for (auto && [id, bin_paths] : seqan::stl::views::enumerate(parse_input(config)))
{
auto reference = read_reference(bin_paths);
fmc::BiFMIndex<4> index{reference, /*samplingRate*/ 16, config.threads};
fmc::BiFMIndex<5> index{reference, /*samplingRate*/ 16, config.threads};

{
std::ofstream os{fmt::format("{}.{}.fmindex", config.output_path.c_str(), id), std::ios::binary};
Expand Down
129 changes: 88 additions & 41 deletions src/search/fmindex.cpp
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Expand Up @@ -3,6 +3,7 @@
// SPDX-License-Identifier: BSD-3-Clause

#include <fmt/format.h>
#include <fmt/ranges.h>

#include <seqan3/io/sequence_file/input.hpp>

Expand All @@ -17,75 +18,121 @@
namespace search
{

fmc::BiFMIndex<4> load_index(config const & config, size_t const id)
template <typename Index>
auto myReconstruct(Index const & index, size_t seqNbr) -> std::vector<uint8_t>
{
fmc::BiFMIndex<4> index{};
//TODO: möglicher weise ist das identisch zu einfach index.C[1]
auto totalNumberOfSeq = index.bwt.rank(index.size(), 0) + index.C[0];
for (size_t i{0}; i < totalNumberOfSeq; ++i)
{
auto idx = std::get<0>(std::get<0>(index.locate(i)));
if (idx == seqNbr)
{
return reconstructText(index, i);
}
}
throw std::runtime_error{"unknown sequence number"};
}

fmc::BiFMIndex<5> load_index(config const & config, size_t const id)
{
fmc::BiFMIndex<5> index{};

{
std::ifstream os{fmt::format("{}.{}.fmindex", config.input_path.c_str(), id), std::ios::binary};
cereal::BinaryInputArchive iarchive{os};
iarchive(index);
}

// {
// fmt::println(" === Reconstruct all ===");
// auto text = fmc::reconstructText(index);
// for (size_t i = 0; i < text.size(); ++i)
// fmt::print("### {} ###\n{}\n", i, fmt::join(text[i], ""));
// }
// {
// fmt::println(" === Reconstruct single ===");
// auto text = fmc::reconstructText(index, 0);
// fmt::print("### 0 ###\n{}\n", fmt::join(text, ""));
// text = fmc::reconstructText(index, 1);
// fmt::print("### 1 ###\n{}\n", fmt::join(text, ""));
// }
// {
// fmt::println(" === Reconstruct alternative ===");
// auto text = myReconstruct(index, 0);
// fmt::print("### 0 ###\n{}\n", fmt::join(text, ""));
// text = myReconstruct(index, 1);
// fmt::print("### 1 ###\n{}\n", fmt::join(text, ""));
// }

return index;
}

void fmindex(config const & config, std::vector<hit> hits, size_t const todo_bin_count)
std::vector<wip_alignment> fmindex(config const & config, std::vector<hit> hits, size_t const todo_bin_count)
{
// todo bin count
// todo capacity
// each slot = 1 bin
// a cart is full if it has 5 elements (hits)
scq::slotted_cart_queue<size_t> queue{{.slots = todo_bin_count, .carts = todo_bin_count, .capacity = 5}};
size_t thread_id{};

auto get_thread = [&]()
alignment_vector res;
{
return std::jthread(
[&, thread_id = thread_id++]()
{
while (true)
scq::slotted_cart_queue<size_t> queue{{.slots = todo_bin_count, .carts = todo_bin_count, .capacity = 5}};
size_t thread_id{};

auto get_thread = [&]()
{
return std::jthread(
[&, thread_id = thread_id++]()
{
scq::cart_future<size_t> cart = queue.dequeue();
if (!cart.valid())
return;
auto [slot, span] = cart.get();
auto index = load_index(config, slot.value);
for (auto idx : span)
while (true)
{
auto & [id, seq, bins] = hits[idx];

auto callback = [&](auto cursor, size_t)
scq::cart_future<size_t> cart = queue.dequeue();
if (!cart.valid())
return;
auto [slot, span] = cart.get();
auto index = load_index(config, slot.value);
for (auto idx : span)
{
for (auto j : cursor)
auto & [id, seq, bins] = hits[idx];

auto callback = [&](auto cursor, size_t)
{
auto [entry, offset] = index.locate(j);
auto [seqId, pos] = entry;
for (auto j : cursor)
{
fmt::print("[{}][{}] found hit in bin {} in seqNo {} at Pos {}\n",
thread_id,
id,
slot.value,
seqId,
pos + offset);
auto [entry, offset] = index.locate(j);
auto [seqId, pos] = entry;
// fmt::print("[{}][{}] found hit in bin {} in seqNo {} at Pos {}\n",
// thread_id,
// id,
// slot.value,
// seqId,
// pos + offset);
res.emplace_back(wip_alignment{.bin = slot.value,
.sequence_number = seqId,
.position = pos + offset,
.seq = seq,
.ref = myReconstruct(index, seqId),
.id = id}); // todo seq is copied
}
}
};
};

fmc::search<true>(index, seq, config.errors, callback);
fmc::search<true>(index, seq, config.errors, callback);
}
}
}
});
};
});
};

std::vector<std::jthread> worker(config.threads);
std::ranges::generate(worker, get_thread);

std::vector<std::jthread> worker(config.threads);
std::ranges::generate(worker, get_thread);
for (auto && [idx, hit] : seqan::stl::views::enumerate(hits))
for (auto bin : hit.bins)
queue.enqueue(scq::slot_id{bin}, idx);

for (auto && [idx, hit] : seqan::stl::views::enumerate(hits))
for (auto bin : hit.bins)
queue.enqueue(scq::slot_id{bin}, idx);
queue.close();
} // Wait for threads to finish

queue.close();
return res.get();
}

} // namespace search
2 changes: 1 addition & 1 deletion src/search/ibf.cpp
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Expand Up @@ -90,7 +90,7 @@ std::vector<hit> ibf(config const & config, size_t & todo_bin_count)
| std::views::transform(
[](auto const & in)
{
return seqan3::to_rank(in);
return seqan3::to_rank(in) + 1u;
}),
std::back_inserter(hits[i].seq));
std::ranges::copy(result, std::back_inserter(hits[i].bins));
Expand Down
74 changes: 73 additions & 1 deletion src/search/search.cpp
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Expand Up @@ -2,16 +2,88 @@
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

#include <fmt/format.h>
#include <fmt/ranges.h>

#include <seqan3/alignment/cigar_conversion/cigar_from_alignment.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/io/sam_file/output.hpp>

#include <fpgalign/search/search.hpp>

namespace search
{

auto format_as(wip_alignment wip)
{
return fmt::format("(bin = {}, seqNo = {}, pos = {}, seq = {:d}, ref = {:d})",
wip.bin,
wip.sequence_number,
wip.position,
fmt::join(wip.seq, ""),
fmt::join(wip.ref, ""));
}

void do_alignment(config const & config, std::vector<wip_alignment> const & wips)
{
seqan3::sam_file_output sam_out{config.output_path,
seqan3::fields<seqan3::field::seq,
seqan3::field::id,
seqan3::field::ref_id,
seqan3::field::ref_offset,
seqan3::field::cigar,
// seqan3::field::qual,
seqan3::field::mapq>{}};

seqan3::configuration const align_config =
seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1_leading{true},
seqan3::align_cfg::free_end_gaps_sequence2_leading{false},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{true},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{false}}
| seqan3::align_cfg::edit_scheme | seqan3::align_cfg::output_alignment{}
| seqan3::align_cfg::output_begin_position{} | seqan3::align_cfg::output_score{};

for (auto & wip : wips)
{
size_t const start = wip.position - static_cast<size_t>(wip.position != 0u);
size_t const length = wip.seq.size();
auto it = std::ranges::next(wip.ref.begin(), start, wip.ref.end());
auto end = std::ranges::next(it, length + 1u, wip.ref.end());
std::span ref_text{it, end};

for (auto && alignment : seqan3::align_pairwise(std::tie(ref_text, wip.seq), align_config))
{
auto cigar = seqan3::cigar_from_alignment(alignment.alignment());
size_t ref_offset = alignment.sequence1_begin_position() + 2 + start;
size_t map_qual = 60u + alignment.score();

sam_out.emplace_back(std::views::transform(wip.seq,
[](auto const in)
{
return seqan3::dna4{}.assign_rank(
static_cast<uint8_t>(in - 1u));
}),
wip.id,
fmt::format("{}", wip.sequence_number), // todo ref storage
ref_offset,
cigar,
// record.base_qualities(),
map_qual);
}
}
}

void search(config const & config)
{
size_t todo_bin_count{};
std::vector<hit> hits = ibf(config, todo_bin_count);
fmindex(config, std::move(hits), todo_bin_count);
auto const res = fmindex(config, std::move(hits), todo_bin_count);
do_alignment(config, res);
// for (auto const & elem : res)
// {
// fmt::print("{}\n", elem);
// }
}

} // namespace search