[med-svn] [Git][med-team/spoa][master] 6 commits: New upstream version 1.1.5
Andreas Tille
gitlab at salsa.debian.org
Mon Jan 28 20:12:52 GMT 2019
Andreas Tille pushed to branch master at Debian Med / spoa
Commits:
fe7cc825 by Andreas Tille at 2019-01-28T19:04:57Z
New upstream version 1.1.5
- - - - -
b53870fb by Andreas Tille at 2019-01-28T19:04:57Z
Update upstream source from tag 'upstream/1.1.5'
Update to upstream version '1.1.5'
with Debian dir aaf1b9c8c2dc3a33dfd0f9e2b591f899d5039f42
- - - - -
c4cb7070 by Andreas Tille at 2019-01-28T19:04:58Z
New upstream version
- - - - -
332c6d71 by Andreas Tille at 2019-01-28T19:04:58Z
debhelper 12
- - - - -
390b4a4d by Andreas Tille at 2019-01-28T19:05:03Z
Standards-Version: 4.3.0
- - - - -
873e98aa by Andreas Tille at 2019-01-28T19:58:39Z
Upstream changed ABI and we stick here to the broken way to set soversion = version but upstream was informed to invent better soversions
https://github.com/rvaser/spoa/issues/14
- - - - -
11 changed files:
- CMakeLists.txt
- README.md
- debian/changelog
- debian/compat
- debian/control
- debian/libspoa1.1.3.symbols → debian/libspoa1.1.5.symbols
- + debian/patches/fix_soversion.patch
- debian/patches/series
- include/spoa/graph.hpp
- src/graph.cpp
- src/main.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -1,5 +1,5 @@
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
=====================================
@@ -4,7 +4,7 @@
[](https://travis-ci.org/rvaser/spoa)
[](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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+spoa (1.1.5-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * debhelper 12
+ * Standards-Version: 4.3.0
+ * Upstream changed ABI and we stick here to the broken way to set
+ soversion = version but upstream was informed to invent better soversions
+ https://github.com/rvaser/spoa/issues/14
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Jan 2019 20:04:58 +0100
+
spoa (1.1.3-4) unstable; urgency=medium
* Set architecture to amd64 since the code is not really portable
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12
=====================================
debian/control
=====================================
@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
cmake,
d-shlibs,
rename,
libbioparser-dev,
libgtest-dev,
zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/spoa
Vcs-Git: https://salsa.debian.org/med-team/spoa.git
Homepage: https://github.com/rvaser/spoa
@@ -27,7 +27,7 @@ Description: SIMD partial order alignment tool
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
-Package: libspoa1.1.3
+Package: libspoa1.1.5
Architecture: amd64
Section: libs
Depends: ${shlibs:Depends},
@@ -47,7 +47,7 @@ Architecture: amd64
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
- libspoa1.1.3 (= ${binary:Version})
+ libspoa1.1.5 (= ${binary:Version})
Description: SIMD partial order alignment library (development files)
Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
=====================================
debian/libspoa1.1.3.symbols → debian/libspoa1.1.5.symbols
=====================================
@@ -1,13 +1,9 @@
-libspoa.so.1.1.3 libspoa1.1.3 #MINVER#
+libspoa.so.1.1.5 libspoa1.1.5 #MINVER#
_ZN4spoa11createGraphEv at Base 1.1.3
_ZN4spoa15AlignmentEngine25align_sequence_with_graphERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt10unique_ptrINS_5GraphESt14default_deleteISA_EE at Base 1.1.3
_ZN4spoa15AlignmentEngineC1ENS_13AlignmentTypeEaaa at Base 1.1.3
_ZN4spoa15AlignmentEngineC2ENS_13AlignmentTypeEaaa at Base 1.1.3
- (optional)_ZN4spoa19SimdAlignmentEngine10initializeINS_14InstructionSetIiEEEEvPKcRKSt10unique_ptrINS_5GraphESt14default_deleteIS7_EEjjj at Base 1.1.3
- (optional)_ZN4spoa19SimdAlignmentEngine10initializeINS_14InstructionSetIsEEEEvPKcRKSt10unique_ptrINS_5GraphESt14default_deleteIS7_EEjjj at Base 1.1.3
_ZN4spoa19SimdAlignmentEngine25align_sequence_with_graphEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteIS4_EE at Base 1.1.3
- (optional)_ZN4spoa19SimdAlignmentEngine5alignINS_14InstructionSetIiEEEESt6vectorISt4pairIiiESaIS6_EEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteISC_EE at Base 1.1.3
- (optional)_ZN4spoa19SimdAlignmentEngine5alignINS_14InstructionSetIsEEEESt6vectorISt4pairIiiESaIS6_EEPKcjRKSt10unique_ptrINS_5GraphESt14default_deleteISC_EE at Base 1.1.3
_ZN4spoa19SimdAlignmentEngine7reallocEjjj at Base 1.1.3
_ZN4spoa19SimdAlignmentEngine8preallocEjj at Base 1.1.3
_ZN4spoa19SimdAlignmentEngineC1ENS_13AlignmentTypeEaaa at Base 1.1.3
@@ -60,12 +56,13 @@ libspoa.so.1.1.3 libspoa1.1.3 #MINVER#
_ZN4spoa5GraphD2Ev at Base 1.1.3
_ZNK4spoa4Node8coverageEv at Base 1.1.3
_ZNK4spoa4Node9successorERjj at Base 1.1.3
- _ZNK4spoa5Graph14print_graphvizEv at Base 1.1.3
_ZNK4spoa5Graph16update_alignmentERSt6vectorISt4pairIiiESaIS3_EERKS1_IiSaIiEE at Base 1.1.3
_ZNK4spoa5Graph22extract_subgraph_nodesERSt6vectorIbSaIbEEjj at Base 1.1.3
_ZNK4spoa5Graph23is_topologically_sortedEv at Base 1.1.3
_ZNK4spoa5Graph38initialize_multiple_sequence_alignmentERSt6vectorIjSaIjEE at Base 1.1.3
_ZNK4spoa5Graph8subgraphEjjRSt6vectorIiSaIiEE at Base 1.1.3
+ _ZNK4spoa5Graph9print_dotERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.5
+ _ZNKSt5ctypeIcE8do_widenEc at Base 1.1.5
_ZNSt10_HashtableIjjSaIjENSt8__detail9_IdentityESt8equal_toIjESt4hashIjENS1_18_Mod_range_hashingENS1_20_Default_ranged_hashENS1_20_Prime_rehash_policyENS1_17_Hashtable_traitsILb0ELb1ELb1EEEE21_M_insert_unique_nodeEmmPNS1_10_Hash_nodeIjLb0EEEm at Base 1.1.3
_ZNSt11_Deque_baseIjSaIjEE17_M_initialize_mapEm at Base 1.1.3
_ZNSt11_Deque_baseIjSaIjEED1Ev at Base 1.1.3
@@ -85,17 +82,12 @@ libspoa.so.1.1.3 libspoa1.1.3 #MINVER#
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.1.3
_ZNSt6vectorISt10shared_ptrIN4spoa4EdgeEESaIS3_EE17_M_realloc_insertIJRS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 1.1.3
_ZNSt6vectorISt10unique_ptrIN4spoa4NodeESt14default_deleteIS2_EESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.1.3
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJRKjiEEEvDpOT_ at Base 1.1.3
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJiRiEEEvDpOT_ at Base 1.1.3
- (optional)_ZNSt6vectorISt4pairIiiESaIS1_EE12emplace_backIJjiEEEvDpOT_ at Base 1.1.3
_ZNSt6vectorISt4pairIiiESaIS1_EE17_M_realloc_insertIJjjEEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.1.3
_ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb at Base 1.1.3
_ZNSt6vectorIiSaIiEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPiS1_EEmRKi at Base 1.1.3
_ZNSt6vectorIjSaIjEE12emplace_backIJRKiEEEvDpOT_ at Base 1.1.3
_ZNSt6vectorIjSaIjEE12emplace_backIJRiEEEvDpOT_ at Base 1.1.3
_ZNSt6vectorIjSaIjEE12emplace_backIJRjEEEvDpOT_ at Base 1.1.3
- (optional)_ZNSt6vectorIjSaIjEE12emplace_backIJiEEEvDpOT_ at Base 1.1.3
- (optional)_ZNSt6vectorIjSaIjEE12emplace_backIJjEEEvDpOT_ at Base 1.1.3
_ZNSt6vectorIjSaIjEE14_M_fill_insertEN9__gnu_cxx17__normal_iteratorIPjS1_EEmRKj at Base 1.1.3
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1.3
_ZTIN4spoa15AlignmentEngineE at Base 1.1.3
=====================================
debian/patches/fix_soversion.patch
=====================================
@@ -0,0 +1,17 @@
+Note: Patch is not activated to not derive to much from upstream
+Description: Invent SOVERSION different from upstream version
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 28 Jan 2019 20:04:58 +0100
+Bug-Upstream: https://github.com/rvaser/spoa/issues/14
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -41,7 +41,7 @@ target_include_directories(spoa_static P
+ set_target_properties(spoa
+ PROPERTIES
+ VERSION ${spoa_VERSION}
+- SOVERSION ${spoa_VERSION})
++ SOVERSION 2)
+
+ install(TARGETS spoa DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ install(TARGETS spoa_static DESTINATION ${CMAKE_INSTALL_LIBDIR})
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
use_debian_packaged_libs.patch
shared_and_static.patch
no_march.patch
+# fix_soversion.patch
=====================================
include/spoa/graph.hpp
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -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"
View it on GitLab: https://salsa.debian.org/med-team/spoa/compare/be43d11ca23357cdddd9740f209e4b6b16549094...873e98aa01d0a3cf19e586f04dbbac5a7211288e
--
View it on GitLab: https://salsa.debian.org/med-team/spoa/compare/be43d11ca23357cdddd9740f209e4b6b16549094...873e98aa01d0a3cf19e586f04dbbac5a7211288e
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