From 18389adb35ff8d0199c89f82dc97f78931164791 Mon Sep 17 00:00:00 2001 From: Neel Basu <20411+neel@users.noreply.github.com> Date: Fri, 18 Jul 2025 13:08:23 +0200 Subject: [PATCH 1/5] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index bb91d7d..53a4474 100644 --- a/README.md +++ b/README.md @@ -45,8 +45,10 @@ make -C build ### Meson (0.60.0+) +Forked from https://github.com/rvaser/spoa + ```bash -git clone https://github.com/rvaser/spoa && cd spoa +git clone https://github.com/neel/spoa && cd spoa meson setup build ninja -C build ``` From bf93639e0698e02c3bb45b0f3a61fccab29070f1 Mon Sep 17 00:00:00 2001 From: Neel Basu <20411+neel@users.noreply.github.com> Date: Fri, 18 Jul 2025 13:08:52 +0200 Subject: [PATCH 2/5] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 53a4474..ef6ae81 100644 --- a/README.md +++ b/README.md @@ -24,8 +24,10 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg ### CMake (3.12+) +Forked from https://github.com/rvaser/spoa + ```bash -git clone https://github.com/rvaser/spoa && cd spoa +git clone https://github.com/neel/spoa && cd spoa cmake -B build -DCMAKE_BUILD_TYPE=Release make -C build ``` From be1d7eafcd33e1b4bc2d7d1fce237fd9e8df1a3b Mon Sep 17 00:00:00 2001 From: Sunanda Bose Date: Fri, 18 Jul 2025 13:10:40 +0200 Subject: [PATCH 3/5] - gap character not fixed --- include/spoa/graph.hpp | 3 +-- src/graph.cpp | 7 +++---- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/include/spoa/graph.hpp b/include/spoa/graph.hpp index 5645766..7833e99 100644 --- a/include/spoa/graph.hpp +++ b/include/spoa/graph.hpp @@ -161,8 +161,7 @@ class Graph { const char* sequence, std::uint32_t sequence_len, const char* quality, std::uint32_t quality_len); - std::vector GenerateMultipleSequenceAlignment( - bool include_consensus = false); + std::vector GenerateMultipleSequenceAlignment(bool include_consensus = false, char gap='-'); std::string GenerateConsensus(); diff --git a/src/graph.cpp b/src/graph.cpp index 44cedd6..f58ae70 100644 --- a/src/graph.cpp +++ b/src/graph.cpp @@ -336,14 +336,13 @@ std::vector Graph::InitializeMultipleSequenceAlignment( return dst; } -std::vector Graph::GenerateMultipleSequenceAlignment( - bool include_consensus) { +std::vector Graph::GenerateMultipleSequenceAlignment(bool include_consensus, char gap) { std::uint32_t row_size = 0; auto node_id_to_column = InitializeMultipleSequenceAlignment(&row_size); std::vector dst; for (std::uint32_t i = 0; i < sequences_.size(); ++i) { - std::string row(row_size, '-'); + std::string row(row_size, gap); auto it = sequences_[i]; while (true) { row[node_id_to_column[it->id]] = decoder_[it->code]; @@ -355,7 +354,7 @@ std::vector Graph::GenerateMultipleSequenceAlignment( } if (include_consensus) { TraverseHeaviestBundle(); - std::string row(row_size, '-'); + std::string row(row_size, gap); for (const auto& it : consensus_) { row[node_id_to_column[it->id]] = decoder_[it->code]; } From 820a2c8ffc3c42f9316d67f34d8afa625e558935 Mon Sep 17 00:00:00 2001 From: Sunanda Bose Date: Fri, 18 Jul 2025 13:13:26 +0200 Subject: [PATCH 4/5] - revert README --- README.md | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ef6ae81..bb91d7d 100644 --- a/README.md +++ b/README.md @@ -24,10 +24,8 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg ### CMake (3.12+) -Forked from https://github.com/rvaser/spoa - ```bash -git clone https://github.com/neel/spoa && cd spoa +git clone https://github.com/rvaser/spoa && cd spoa cmake -B build -DCMAKE_BUILD_TYPE=Release make -C build ``` @@ -47,10 +45,8 @@ make -C build ### Meson (0.60.0+) -Forked from https://github.com/rvaser/spoa - ```bash -git clone https://github.com/neel/spoa && cd spoa +git clone https://github.com/rvaser/spoa && cd spoa meson setup build ninja -C build ``` From f783a00746850eb5ad730f769fa134d9f32215b9 Mon Sep 17 00:00:00 2001 From: Sunanda Bose <20411+neel@users.noreply.github.com> Date: Fri, 18 Jul 2025 13:42:45 +0200 Subject: [PATCH 5/5] - MSVC compilation issue fixed --- CMakeLists.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 2f7422e..4ba58f1 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -4,7 +4,10 @@ project(spoa VERSION 4.1.4 LANGUAGES CXX DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.") -set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic") +if(NOT MSVC) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic") +endif() + set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_EXTENSIONS OFF)