New upstream version 1.1.5 (fe7cc825) · Commits · Debian Med / spoa

CMakeLists.txt

+1 −1

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		cmake_minimum_required(VERSION 3.2)
		project(spoa LANGUAGES CXX VERSION 1.1.3)
		project(spoa LANGUAGES CXX VERSION 1.1.5)

		include(GNUInstallDirs)

README.md

+7 −2

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		@@ -4,7 +4,7 @@
		[![Build status for c++/clang++](https://travis-ci.org/rvaser/spoa.svg?branch=master)](https://travis-ci.org/rvaser/spoa)
		[![Published in Genome Research](https://img.shields.io/badge/published%20in-Genome%20Research-blue.svg)](https://doi.org/10.1101/gr.214270.116)

		Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap). It supports Intel SSE4.1+ and AVX2 (marginally faster due to high latency shifts) vectorization.
		Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap). It supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts).

		## Dependencies

		@@ -39,6 +39,8 @@ Optionally, you can run `sudo make install` to install spoa library (and executa

		*Note*: if you omitted `--recursive` from `git clone`, run `git submodule init` and `git submodule update` before proceeding with compilation.

		To build unit tests add `-Dspoa_build_tests=ON` while running `cmake`. After installation, an executable named `spoa_test` will be created in `build/bin`.

		## Usage

		Usage of spoa is as following:
		@@ -46,7 +48,8 @@ Usage of spoa is as following:
		spoa [options ...] <sequences>

		<sequences>
		input file in FASTA/FASTQ format containing sequences
		input file in FASTA/FASTQ format (can be compressed with gzip)
		containing sequences

		options:
		-m, --match <int>
		@@ -70,6 +73,8 @@ Usage of spoa is as following:
		0 - consensus
		1 - multiple sequence alignment
		2 - 0 & 1
		-d, --dot <file>
		output file for the final POA graph in DOT format
		--version
		prints the version number
		-h, --help

include/spoa/graph.hpp

+1 −1

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		@@ -78,7 +78,7 @@ public:
		void update_alignment(Alignment& alignment,
		const std::vector<int32_t>& subgraph_to_graph_mapping) const;

		void print_graphviz() const;
		void print_dot(const std::string& path) const;

		friend std::unique_ptr<Graph> createGraph();
		private:

src/graph.cpp

+23 −12

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		@@ -8,6 +8,7 @@
		#include <assert.h>
		#include <algorithm>
		#include <stack>
		#include <fstream>

		#include "spoa/graph.hpp"

		@@ -679,7 +680,13 @@ void Graph::update_alignment(Alignment& alignment,
		}
		}

		void Graph::print_graphviz() const {
		void Graph::print_dot(const std::string& path) const {

		if (path.empty()) {
		return;
		}

		std::ofstream out(path);

		std::vector<int32_t> in_consensus(nodes_.size(), -1);
		int32_t rank = 0;
		@@ -687,30 +694,34 @@ void Graph::print_graphviz() const {
		in_consensus[id] = rank++;
		}

		printf("digraph %u {\n", num_sequences_);
		printf(" graph [rankdir=LR]\n");
		out << "digraph " << num_sequences_ << " {" << std::endl;
		out << " graph [rankdir=LR]" << std::endl;
		for (uint32_t i = 0; i < nodes_.size(); ++i) {
		printf(" %u [label = \"%u - %c\"", i, i, decoder_[nodes_[i]->code_]);
		out << " " << i << " [label = \"" << i << " - ";
		out << static_cast<char>(decoder_[nodes_[i]->code_]) << "\"";
		if (in_consensus[i] != -1) {
		printf(", style=filled, fillcolor=goldenrod1");
		out << ", style=filled, fillcolor=goldenrod1";
		}
		printf("]\n");
		out << "]" << std::endl;

		for (const auto& edge: nodes_[i]->out_edges_) {
		printf(" %u -> %u [label = \"%lu\"", i, edge->end_node_id_,
		edge->total_weight_);
		out << " " << i << " -> " << edge->end_node_id_;
		out << " [label = \"" << edge->total_weight_ << "\"";
		if (in_consensus[i] + 1 == in_consensus[edge->end_node_id_]) {
		printf(", color=goldenrod1");
		out << ", color=goldenrod1";
		}
		printf("]\n");
		out << "]" << std::endl;
		}
		for (const auto& aid: nodes_[i]->aligned_nodes_ids_) {
		if (aid > i) {
		printf(" %u -> %u [style = dotted, arrowhead = none]\n", i, aid);
		out << " " << i << " -> " << aid;
		out << " [style = dotted, arrowhead = none]" << std::endl;
		}
		}
		}
		printf("}\n");
		out << "}" << std::endl;

		out.close();
		}

		}

src/main.cpp

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		@@ -7,7 +7,7 @@
		#include "spoa/spoa.hpp"
		#include "bioparser/bioparser.hpp"

		static const char* version = "v1.1.3";
		static const char* version = "v1.1.5";

		static struct option options[] = {
		{"match", required_argument, 0, 'm'},
		@@ -15,6 +15,7 @@ static struct option options[] = {
		{"gap", required_argument, 0, 'g'},
		{"algorithm", required_argument, 0, 'l'},
		{"result", required_argument, 0, 'r'},
		{"dot", required_argument, 0, 'd'},
		{"version", no_argument, 0, 'v'},
		{"help", no_argument, 0, 'h'},
		{0, 0, 0, 0}
		@@ -31,8 +32,10 @@ int main(int argc, char** argv) {
		uint8_t algorithm = 0;
		uint8_t result = 0;

		std::string dot_path = "";

		char opt;
		while ((opt = getopt_long(argc, argv, "m:x:g:l:r:h", options, nullptr)) != -1) {
		while ((opt = getopt_long(argc, argv, "m:x:g:l:r:d:h", options, nullptr)) != -1) {
		switch (opt) {
		case 'm':
		match = atoi(optarg);
		@@ -49,6 +52,9 @@ int main(int argc, char** argv) {
		case 'r':
		result = atoi(optarg);
		break;
		case 'd':
		dot_path = optarg;
		break;
		case 'v':
		printf("%s\n", version);
		exit(0);
		@@ -66,22 +72,30 @@ int main(int argc, char** argv) {
		exit(1);
		}

		std::string input_path = argv[optind];
		auto extension = input_path.substr(std::min(input_path.rfind('.'),
		input_path.size()));
		std::string sequences_path = argv[optind];

		auto is_suffix = [](const std::string& src, const std::string& suffix) -> bool {
		if (src.size() < suffix.size()) {
		return false;
		}
		return src.compare(src.size() - suffix.size(), suffix.size(), suffix) == 0;
		};

		std::unique_ptr<bioparser::Parser<spoa::Sequence>> sparser = nullptr;

		if (extension == ".fasta" \|\| extension == ".fa") {
		if (is_suffix(sequences_path, ".fasta") \|\| is_suffix(sequences_path, ".fa") \|\|
		is_suffix(sequences_path, ".fasta.gz") \|\| is_suffix(sequences_path, ".fa.gz")) {
		sparser = bioparser::createParser<bioparser::FastaParser, spoa::Sequence>(
		input_path);
		} else if (extension == ".fastq" \|\| extension == ".fq") {
		sequences_path);
		} else if (is_suffix(sequences_path, ".fastq") \|\| is_suffix(sequences_path, ".fq") \|\|
		is_suffix(sequences_path, ".fastq.gz") \|\| is_suffix(sequences_path, ".fq.gz")) {
		sparser = bioparser::createParser<bioparser::FastqParser, spoa::Sequence>(
		input_path);
		sequences_path);
		} else {
		fprintf(stderr, "[spoa::] error: "
		"file %s has unsupported format extension (valid extensions: "
		".fasta, .fa, .fastq, .fq)!\n", input_path.c_str());
		".fasta, .fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)!\n",
		sequences_path.c_str());
		exit(1);
		}

		@@ -120,6 +134,8 @@ int main(int argc, char** argv) {
		}
		}

		graph->print_dot(dot_path);

		return 0;
		}

		@@ -128,7 +144,8 @@ void help() {
		"usage: spoa [options ...] <sequences>\n"
		"\n"
		" <sequences>\n"
		" input file in FASTA/FASTQ format containing sequences\n"
		" input file in FASTA/FASTQ format (can be compressed with gzip)\n"
		" containing sequences\n"
		"\n"
		" options:\n"
		" -m, --match <int>\n"
		@@ -152,6 +169,8 @@ void help() {
		" 0 - consensus\n"
		" 1 - multiple sequence alignment\n"
		" 2 - 0 & 1\n"
		" -d, --dot <file>\n"
		" output file for the final POA graph in DOT format\n"
		" --version\n"
		" prints the version number\n"
		" -h, --help\n"