[med-svn] [Git][med-team/kissplice][master] 5 commits: New upstream version 2.6.7
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Aug 7 10:23:21 BST 2024
Andreas Tille pushed to branch master at Debian Med / kissplice
Commits:
c92a247a by Andreas Tille at 2024-08-07T11:18:15+02:00
New upstream version 2.6.7
- - - - -
fbfdcc89 by Andreas Tille at 2024-08-07T11:18:15+02:00
routine-update: New upstream version
- - - - -
4d304f4b by Andreas Tille at 2024-08-07T11:18:18+02:00
Update upstream source from tag 'upstream/2.6.7'
Update to upstream version '2.6.7'
with Debian dir d9fc5205c8288b1a563370a08940be78f2760bca
- - - - -
d0d08300 by Andreas Tille at 2024-08-07T11:18:18+02:00
routine-update: Standards-Version: 4.7.0
- - - - -
e2f57501 by Andreas Tille at 2024-08-07T11:21:59+02:00
Close bugs and upload to unstable
- - - - -
18 changed files:
- CMakeLists.txt
- ChangeLog
- README.md
- debian/changelog
- debian/control
- doc/user_guide.in.tex
- kissplice.in.py
- modules/ClusterBubbles.cpp
- modules/EntropyFilter.cpp
- modules/ErrorRemoval.cpp
- modules/NGraph.cpp
- modules/Utils.cpp
- modules/Utils.h
- modules/run.cpp
- tests/integration_tests/kisspliceDBGTest.py
- thirdparty/kissreads/src/commons.cpp
- thirdparty/kissreads/src/kissReads.cpp
- thirdparty/kissreads/src/outputs.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -3,11 +3,11 @@ cmake_minimum_required(VERSION 3.9)
project(
kissplice
- VERSION 2.6.3 # Definition which is propagated through PROJECT_VERSION
+ VERSION 2.6.7 # Definition which is propagated through PROJECT_VERSION
LANGUAGES CXX
)
-set(CMAKE_CXX_STANDARD 11) # Default to C++11 for C++ targets
+set(CMAKE_CXX_STANDARD 14) # Default to C++14 for C++ targets
set(CMAKE_CXX_STANDARD_REQUIRED ON) # Fail if not supported (very old compiler at this point)
# Build type, should be set by user. Useful predefined values (see `cmake -LH`): Debug, Release, RelWithDebInfo.
=====================================
ChangeLog
=====================================
@@ -1,7 +1,19 @@
+2024-06-06 Francois Gindraud <francois.gindraud at inria.fr>
+ * 2.6.6 -> 2.6.7
+ Bug fix : stop with clear message when 0 BCC
+
+2024-05-30 Francois Gindraud <francois.gindraud at inria.fr>
+ * 2.6.5 -> 2.6.6
+ MacOS bug fixes
+
+2024-05-24 Francois Gindraud <francois.gindraud at inria.fr>
+ * 2.6.4 -> 2.6.5
+ Bug fixes so that testsuite runs on MacOS
+
2024-05-23 Francois Gindraud <francois.gindraud at inria.fr>
* 2.6.3 -> 2.6.4
Bug fix for building kissplice and bcalm on ARM MacOS.
- Improvements to switch bteween bundled and system mode for bcalm.
+ Improvements to switch between bundled and system mode for bcalm.
2024-04-04 Francois Gindraud <francois.gindraud at inria.fr>
* 2.6.2 -> 2.6.3
=====================================
README.md
=====================================
@@ -17,6 +17,16 @@ kissplice --help
## Conda
Kissplice is available in conda in the [bioconda channel](https://bioconda.github.io/).
Bioconda creates packages for Linux (x86_64 and arm64) and MacOS (x86_64 = intel macs before M1).
+```bash
+conda install -c conda-forge -c bioconda kissplice
+```
+
+## Homebrew (MacOS)
+Kissplice is available as a brew formula in [brewsci/bio](https://github.com/brewsci/homebrew-bio) in MacOS.
+This is the only packaged option for ARM MacOS (M1 and later).
+```bash
+brew install brewsci/bio/kissplice
+```
## Docker
You can find the latest version of KisSplice, KisSplice2RefGenome and KissDE [on Docker Hub](https://hub.docker.com/repository/docker/dwishsan/kissplice-pipeline).
@@ -33,14 +43,14 @@ kissplice-binary-ubuntu-<version>/bin/kissplice --help
## Build from source
Required dependencies:
- cmake >= 3.9
-- C/C++11 compiler toolchain (binutils, gcc or clang)
+- C/C++14 compiler toolchain (binutils, gcc or clang)
- python3 to run kissplice
Optional dependencies:
- [bcalm](https://github.com/GATB/bcalm) >= v2.2.2. A locally compiled version of bcalm can instead be used by passing `-DUSE_BUNDLED_BCALM=ON` to cmake for convenience, but requires git.
- latex toolchain : only if you request to build the user guide by passing `-DUSER_GUIDE=ON` to cmake
-The following commands assume you are a user that is not familiar with cmake, and wants a local install from source with only the required dependencies (useful for targets like Arm MacOS where no package exists yet).
+The following commands assume you are a user that is not familiar with cmake, and wants a local install from source with only the required dependencies.
If you are a developper or a maintainer of a package, see the [detailed cmake documentation](readme.cmake.md).
Download a *source code* archive from the latest [release](https://gitlab.inria.fr/erable/kissplice/-/releases) and uncompress it.
=====================================
debian/changelog
=====================================
@@ -1,10 +1,15 @@
-kissplice (2.6.4-1) UNRELEASED; urgency=medium
+kissplice (2.6.7-1) unstable; urgency=medium
- * New upstream version
+ [ François Gindraud ]
* Propagate upstream build system changes for bcalm and guide
* Fix dh_auto_clean
- -- François Gindraud <francois.gindraud at inria.fr> Thu, 23 May 2024 17:39:12 +0200
+ [ Andreas Tille ]
+ * New upstream version
+ Closes: #1073482, #1074658
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 07 Aug 2024 11:19:03 +0200
kissplice (2.6.2-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
texlive-latex-recommended,
bcalm <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/kissplice
Vcs-Git: https://salsa.debian.org/med-team/kissplice.git
Homepage: https://kissplice.prabi.fr/
=====================================
doc/user_guide.in.tex
=====================================
@@ -103,7 +103,7 @@ kissplice-binary-ubuntu-<version>/bin/kissplice --help
Required dependencies :
\begin{itemize}
\item cmake >= 3.9
-\item C/C++11 compiler toolchain (binutils, gcc or clang)
+\item C/C++14 compiler toolchain (binutils, gcc or clang)
\item python3 to run kissplice
\item git
\end{itemize}
=====================================
kissplice.in.py
=====================================
@@ -95,7 +95,7 @@ WSLIDE=41 # Right slide of the window on the sequence
# SCRIPT_BINDIR : absolute path to the main executable (this file), computed at runtime
# @KISSPLICE_BINDIR_TO_INTERNAL_BINDIR@ : relative path from main script to internal binaries, set by cmake
# INTERNAL_BINDIR : absolute path to the secondary executables (eg ks_kissreads)
-SCRIPT_BINDIR = os.path.dirname(os.path.abspath(__file__))
+SCRIPT_BINDIR = os.path.dirname(os.path.realpath(__file__))
INTERNAL_BINDIR = os.path.realpath(os.path.join(SCRIPT_BINDIR, "@KISSPLICE_BINDIR_TO_INTERNAL_BINDIR@"))
# Where to find bcalm ; BCALM_PACKAGING_MODE is set by cmake to either 'bundled' or 'system'.
BCALM_PATH = os.path.join(INTERNAL_BINDIR, "bcalm") if "@BCALM_PACKAGING_MODE@" == "bundled" else "bcalm"
@@ -557,7 +557,7 @@ def splitT1T234(fName, fNameT1, fNameT234):
f=open(fName,"r")
f1=open(fNameT1,"w")
f234=open(fNameT234,"w")
- retype = re.compile('Type_\d+')
+ retype = re.compile(r"Type_\d+")
line=f.readline()
while line:
t=retype.search(line).group()
@@ -1206,7 +1206,7 @@ def check_read_coverage_and_sort_all_bubbles(readfiles, workdir, outdir, kval, o
l = cofile.readlines()
l.sort(reverse=True)
cofile.close()
- retype = re.compile('Type_\d+')
+ retype = re.compile(r"Type_\d+")
for event in l:
try:
type = retype.search(event).group()
@@ -1250,7 +1250,7 @@ def sort_all_bubbles(readfiles, workdir, outdir, kval, output_snps, infix_name,
concatenate_graph_all_log_bcc_to_all_bcc_type0(workdir, kval, output_snps)
- retype = re.compile('Type_\d+')
+ retype = re.compile(r"Type_\d+")
eventsName = ["type_0a", "type_0b", "type_1", "type_2", "type_3", "type_4"]
filel = []
for i in range(0,6):
=====================================
modules/ClusterBubbles.cpp
=====================================
@@ -8,9 +8,6 @@
#include <algorithm>
using namespace std;
-#define MIN(a,b) ((a) < (b) ? (a) : (b))
-#define MIN3(a,b,c) ((a) < (b) ? ((a) < (c) ? (a) : (c)) : ((b) < (c) ? (b) : (c)))
-
struct block {
string l[4], bcc;
double rank;
@@ -197,7 +194,7 @@ int edit_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t n
d1 = *(dp - 1) + 1;// insertion
d2 = *(dp - l2 - 1) + 1;// deletion
d3 = *(dp - l2 - 2) + 1;// substitution
- *dp = MIN3(d1, d2, d3);
+ *dp = std::min(d1, std::min(d2, d3));
}
}
}
=====================================
modules/EntropyFilter.cpp
=====================================
@@ -8,9 +8,6 @@
#include <algorithm>
using namespace std;
-#define MIN(a,b) ((a) < (b) ? (a) : (b))
-#define MIN3(a,b,c) ((a) < (b) ? ((a) < (c) ? (a) : (c)) : ((b) < (c) ? (b) : (c)))
-
struct block {
string l[4], bcc;
double rank;
=====================================
modules/ErrorRemoval.cpp
=====================================
@@ -1,11 +1,10 @@
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include <string>
-#include <stdlib.h>
+#include <cstdlib>
#include <vector>
#include "Utils.h"
#include "LabelledCEdge.h"
-#include <iostream>
#include <fstream>
#define MAX 1024
@@ -108,20 +107,19 @@ int findNode(char *query, vector<NodeSeq>& nodes)
return -1;
}
-void readAbundanceFile (char* abundanceFileName, vector<double> &abundances) {
- ifstream abundanceFile(abundanceFileName);
+void readAbundanceFile (char* abundanceFileName, std::vector<double> &abundances) {
+ auto abundanceFile = std::ifstream(abundanceFileName);
if (!abundanceFile) {
- cerr << "Error opening " << abundanceFileName << endl;
+ std::fprintf(stderr, "Error opening %s\n", abundanceFileName);
exit(1);
}
- double abundance;
+ double abundance = 0;
- while (abundanceFile >> abundance)
+ while (abundanceFile >> abundance) {
abundances.push_back(abundance);
-
- abundanceFile.close();
+ }
}
int findEdge(vector<LabelledCEdge>& allEdges, LabelledCEdge e)
=====================================
modules/NGraph.cpp
=====================================
@@ -125,8 +125,8 @@ NGraph::NGraph( CGraph& cgraph, vector<char *>& seqs,
//~ printf( "contructing %s %s (0x%x, 0x%x)\n", seqs[u], seqs[v], seqs[u], seqs[v] );
//~ getchar();
- insert_node( to_str(u), to_str( seqs[u] ) );
- insert_node( to_str(v), to_str( seqs[v] ) );
+ insert_node(std::to_string(u), seqs[u]);
+ insert_node(std::to_string(v), seqs[v]);
insert_bidirected_edges( all_edges, edges[i] );
edges[i].swap_ends();
@@ -236,7 +236,7 @@ void NGraph::insert_bidirected_edges( vector<LabelledCEdge>& all_edges, CEdge ed
{
int u = it->getFirst();
int v = it->getSecond();
- insert_edge( to_str(u), to_str(v), to_str(it->label) );
+ insert_edge(std::to_string(u), std::to_string(v), it->label);
}
}
@@ -978,7 +978,7 @@ void read_graph_edges(NGraph& g, FILE* edge_file)
//while (p != NULL)
// p = strtok(NULL, "\t\n");
- g.insert_edge(to_str(u),to_str(v),to_str(label));
+ g.insert_edge(u, v, label);
}
}
@@ -1008,7 +1008,7 @@ void read_graph_nodes(NGraph& g, FILE* node_file)
p = strtok(NULL, "\t\n");
strcpy(seq, p);
- g.insert_node(to_str(str), to_str(seq));
+ g.insert_node(str, seq);
}
}
/*!
@@ -1062,7 +1062,7 @@ void read_graph_edges_new(NGraph& g, FILE* info_file, FILE* contents_file, FILE
//while (p != NULL)
// p = strtok(NULL, "\t\n");
- g.insert_edge(to_str(u),to_str(v),to_str(label));
+ g.insert_edge(u, v, label);
}
}
@@ -1109,7 +1109,7 @@ void read_graph_nodes_new(NGraph& g, FILE* info_file, FILE* contents_file, FILE
p = strtok(NULL, "\t\n");
strcpy(seq, p);
- g.insert_node(to_str(str), to_str(seq));
+ g.insert_node(str, seq);
}
}
@@ -1128,7 +1128,7 @@ NGraph remove_marked_nodes( NGraph& g, bool* filter, bool value )
if ( filter[u] == value )
{
string u_sequence = g.getSequence(u);
- new_g.insert_node(to_str(u), u_sequence);
+ new_g.insert_node(std::to_string(u), u_sequence);
if ( filter[u] == value )
{
list<NEdge>::const_iterator it;
@@ -1136,7 +1136,7 @@ NGraph remove_marked_nodes( NGraph& g, bool* filter, bool value )
{
if ( filter[it->get_node()] == value )
{
- new_g.insert_edge( to_str(u), to_str(it->get_node()), it->get_labels() );
+ new_g.insert_edge(std::to_string(u), std::to_string(it->get_node()), it->get_labels());
}
}
}
=====================================
modules/Utils.cpp
=====================================
@@ -1,23 +1,10 @@
#include <string>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
#include <algorithm>
#include "Utils.h"
using namespace std;
-string to_str( char buf[] )
-{
- string str = buf;
- return str;
-}
-
-string to_str( int u )
-{
- char buffer[MAX];
- sprintf(buffer, "%d", u);
- return to_str(buffer);
-}
-
char complement(char b)
{
switch(b)
@@ -104,7 +91,7 @@ int edit_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t n
d1 = *(dp - 1) + 1;// insertion
d2 = *(dp - l2 - 1) + 1;// deletion
d3 = *(dp - l2 - 2) + 1;// substitution
- *dp = MIN3(d1, d2, d3);
+ *dp = std::min(d1, std::min(d2, d3));
}
}
}
@@ -162,3 +149,12 @@ string toLowerContext( const string &sequence, const int contextFirst, const int
transform( contextR.begin(), contextR.end(), contextR.begin(), ::tolower);
return contextL + varS + contextR;
}
+
+File File::open_path(const char* path, const char* mode) {
+ auto ptr = std::unique_ptr<std::FILE, Deleter>{std::fopen(path, mode), Deleter{}};
+ if(ptr == nullptr) {
+ std::fprintf(stderr, "Error: could not open file %s (mode=%s)\n", path, mode);
+ std::exit(EXIT_FAILURE);
+ }
+ return File{std::move(ptr)};
+}
=====================================
modules/Utils.h
=====================================
@@ -2,15 +2,13 @@
#define UTILS_H
#include <string>
+#include <memory>
+#include <vector>
+
#define MAX 1024
#define NUMBEROFFILES 128
-#define MIN(a,b) ((a) < (b) ? (a) : (b))
-#define MIN3(a,b,c) ((a) < (b) ? ((a) < (c) ? (a) : (c)) : ((b) < (c) ? (b) : (c)))
using namespace std;
-string to_str( char buf[] );
-string to_str( int u );
-
int edit_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t nmemb, int (*comp)(const void*, const void*));
int hamming_distance(const void *s1, size_t l1, const void *s2, size_t l2, size_t nmemb, int (*comp)(const void*, const void*));
int comp(const void *a, const void *b);
@@ -21,4 +19,50 @@ char reverse_dir(char dir);
FILE* open_file( char* filename );
string toLowerContext( const string &sequence, const int contextFirst, const int contextLast);
+
+// Wrap std::FILE* in a std::unique_ptr for automatic close on destruction.
+struct File {
+ struct Deleter {
+ void operator()(std::FILE* ptr) { std::fclose(ptr); }
+ };
+ std::unique_ptr<std::FILE, Deleter> file_ptr;
+
+ // Access raw file pointer
+ std::FILE* get_ptr() const { return file_ptr.get(); }
+ explicit operator std::FILE*() const { return file_ptr.get(); }
+
+ // Disable default constructor to force use of File::open_*() methods to open a file.
+ File() = delete;
+
+ // Open a file at path. Stops program and print error message on failure.
+ static File open_path(const char* path, const char* mode);
+ static File open_path(const std::string & path, const char* mode) {
+ return File::open_path(path.c_str(), mode);
+ }
+
+ // Format a path using sprintf then open
+ template<typename... Args> static File open_path_sprintf(const char* path_format, const char* mode, Args ...args) {
+ char path[1024];
+ int written = std::snprintf(path, 1024, path_format, args...);
+ if(written < 1024) {
+ return File::open_path(path, mode);
+ } else {
+ auto length = static_cast<std::size_t>(std::snprintf(nullptr, 0, path_format, args...));
+ auto buffer = std::vector<char>(length + 1);
+ std::snprintf(buffer.data(), buffer.size(), path_format, args...);
+ return File::open_path(buffer.data(), mode);
+ }
+ }
+
+ // Just forward to fprintf
+ template<typename... Args> int fprintf(const char* format, Args ...args) const {
+ return std::fprintf(this->get_ptr(), format, args...);
+ }
+
+ // Force close the file early
+ void close() {
+ this->file_ptr.reset();
+ }
+};
+
#endif
=====================================
modules/run.cpp
=====================================
@@ -51,12 +51,11 @@
// ===========================================================================
// Include Libraries
// ===========================================================================
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <iostream>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <vector>
-
+#include <memory>
// ===========================================================================
// Include Project Files
@@ -68,9 +67,6 @@
#include "SplitBcc.h"
#include "Utils.h"
-#define MAX 1024
-
-
// ===========================================================================
// Define Miscellaneous Functions
// ===========================================================================
@@ -78,35 +74,24 @@
void read_edges_and_nodes( char* edges_fname, char* nodes_fname, const int k,
vector<LabelledCEdge>& allEdges, vector<char*>& seqs )
{
- FILE* edge_file = open_file(edges_fname);
- FILE* node_file = open_file(nodes_fname);
-
- read_edge_file( edge_file, allEdges );
- read_node_file( node_file, seqs, k );
-
- fclose( edge_file );
- fclose( node_file );
+ File edge_file = File::open_path(edges_fname, "r");
+ File node_file = File::open_path(nodes_fname, "r");
+ read_edge_file( edge_file.get_ptr(), allEdges );
+ read_node_file( node_file.get_ptr(), seqs, k );
}
int main( int argc, char** argv )
{
- vector<char*> seqs;
-
- vector<LabelledCEdge> allEdges;
-
- string base_name = "./bcc/graph";
-
+ const char* base_name = "./bcc/graph";
bool output_context = false;
- if ( argc < 4 )
- {
+ if (argc < 4) {
fprintf( stderr, "Wrong number of arguments!\n" );
fprintf( stderr, "Usage: ./run_modules edge_file node_file k_value path_to_output [--output-context]\n" );
- return 0;
+ return EXIT_SUCCESS;
}
- if ( argc >= 5 )
- {
+ if (argc >= 5) {
base_name = argv[4];
}
@@ -114,90 +99,57 @@ int main( int argc, char** argv )
{
output_context = true;
}
- // CGraph graph;
- int k_value = atoi( argv[3] );
+ const int k_value = atoi( argv[3] );
// Read input files
+ std::vector<char*> seqs;
+ std::vector<LabelledCEdge> allEdges;
read_edges_and_nodes( argv[1], argv[2], k_value, allEdges, seqs );
- // Creating & Initializing the graph with the edges reads
- CGraph graph( (int)seqs.size(), allEdges, k_value );
+ // Creating & Initializing the graph with the edges reads
+ CGraph graph {(int)seqs.size(), allEdges, k_value};
// Decompose graph into BCCs
fprintf(stdout, "Searching biconnected components...\n");
- vector< vector<CEdge> > bcc = find_bcc(graph);
- fprintf( stdout, "Number of biconnected components found: %d\n\n", (int)bcc.size() );
-
-
+ std::vector<std::vector<CEdge>> bcc = find_bcc(graph);
+ fprintf(stdout, "Number of biconnected components found: %zu\n\n", bcc.size());
graph.destroy_adj_list();
- NGraph* component;
-
- ////////////////////////////
- ////////////////////////////
- ////////////////////////////
- // IO optimization (start)
- ////////////////////////////
// P1 - descriptor files
- char contents_edge_fname[1024];
- char contents_node_fname[1024];
- sprintf( contents_edge_fname, "%s_contents_edges_bcc", base_name.c_str());
- sprintf( contents_node_fname, "%s_contents_nodes_bcc", base_name.c_str());
- FILE *contents_edge_file;
- FILE *contents_node_file;
- contents_edge_file = fopen(contents_edge_fname,"w");
- contents_node_file = fopen(contents_node_fname,"w");
+ File contents_edge_file = File::open_path_sprintf("%s_contents_edges_bcc", "w", base_name);
+ File contents_node_file = File::open_path_sprintf("%s_contents_nodes_bcc", "w", base_name);
int lines_written_edges = 0;
int lines_written_nodes = 0;
- fprintf( contents_edge_file, "%d\n",lines_written_edges );
- fprintf( contents_node_file, "%d\n",lines_written_nodes );
+ contents_edge_file.fprintf("%d\n", lines_written_edges);
+ contents_node_file.fprintf("%d\n", lines_written_nodes);
// P2 - data files
- int number_of_files_max;
- int records_per_file;
- if ((int)bcc.size()==1){
- number_of_files_max = 1;
- records_per_file = 1;
+ // Optimization : write one bcc data per file, unless this would exceed NUMBEROFFILES in which case multiple are written per file.
+ // FIXME find a less convoluted way to deal with that
+ int output_bcc_file_count;
+ int records_per_bcc_file;
+ if (bcc.size() == 0) {
+ std::fprintf(stderr, "Warning: No BCC to handle, stopping\n");
+ return EXIT_FAILURE;
+ } else if (bcc.size() == 1) {
+ output_bcc_file_count = 1;
+ records_per_bcc_file = 1;
+ } else {
+ output_bcc_file_count = std::min(static_cast<int>(bcc.size()), NUMBEROFFILES);
+ records_per_bcc_file = (int)bcc.size() / (output_bcc_file_count-1); // this division may have a remainder, then extra file (+1) required
}
- else{
- if ((int)bcc.size()<NUMBEROFFILES)
- number_of_files_max = (int)bcc.size();
- else
- number_of_files_max = NUMBEROFFILES;
- records_per_file = (int)bcc.size()/(number_of_files_max-1); // this division may have a remainder, then extra file (+1) required
- }
- char total_edge_fname[1024];
- char total_node_fname[1024];
- char total_log_fname[1024];
- char info_snp_fname[1024];
- FILE *total_edge_file[number_of_files_max];
- FILE *total_node_file[number_of_files_max];
- FILE *total_log_file;
- FILE *info_snp_file;
- int ii = 0;
- sprintf( total_edge_fname, "%s_all_edges_bcc_%d", base_name.c_str(), ii+1 );
- total_edge_file[ii] = fopen(total_edge_fname,"w");
- sprintf( total_node_fname, "%s_all_nodes_bcc_%d", base_name.c_str(), ii+1 );
- total_node_file[ii] = fopen(total_node_fname, "w");
- sprintf( total_log_fname, "%s_all_log_bcc", base_name.c_str() );
- total_log_file = fopen(total_log_fname, "w");
- sprintf( info_snp_fname, "%s_info_snp_bcc", base_name.c_str() );
- info_snp_file = fopen(info_snp_fname, "w");
-
- // P3 - ascii info file to get all parameters to read the big files
- char info_fname[1024];
- FILE *info_file;
- sprintf( info_fname, "%s_info_bcc", base_name.c_str());
- info_file = fopen(info_fname,"w");
- fprintf(info_file, "%d \n",(int)bcc.size() );
- fprintf(info_file, "%d \n",records_per_file );
+
+ int current_bcc_file_id = 0;
+ File current_total_edge_file = File::open_path_sprintf("%s_all_edges_bcc_%d", "w", base_name, current_bcc_file_id+1);
+ File current_total_node_file = File::open_path_sprintf("%s_all_nodes_bcc_%d", "w", base_name, current_bcc_file_id+1);
- ///////////////////////////
- // IO optimization (end)
- ///////////////////////////
- ///////////////////////////
- ///////////////////////////
+ File total_log_file = File::open_path_sprintf("%s_all_log_bcc", "w", base_name);
+ File info_snp_file = File::open_path_sprintf("%s_info_snp_bcc", "w", base_name);
+ // P3 - ascii info file to get all parameters to read the big files
+ File info_file = File::open_path_sprintf("%s_info_bcc", "w", base_name);
+ info_file.fprintf("%zu\n", bcc.size());
+ info_file.fprintf("%d\n", records_per_bcc_file);
// For each BCC, ...
for ( int i = 0 ; i < (int)bcc.size() ; i++ )
@@ -205,103 +157,61 @@ int main( int argc, char** argv )
fprintf(stdout, "Processing component %d...\n", i+1);
// Build uncompact graph corresponding to current BCC
- component = new NGraph( graph, seqs, allEdges, bcc[i] );
-
- fprintf( stdout, "Initial size: %d nodes.\n", (int)component->getNbNodes() );
+ auto component = NGraph(graph, seqs, allEdges, bcc[i]);
+ fprintf(stdout, "Initial size: %d nodes.\n", component.getNbNodes() );
// Compress linear paths of size > 2
fprintf(stdout, "Compressing linear paths...\n");
- int original_size = (int)component->getNbNodes();
- component->compress_all_paths();
- fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - (int)component->getNbNodes() );
-
+ int original_size = component.getNbNodes();
+ component.compress_all_paths();
+ fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - component.getNbNodes() );
// Compress bubbles
fprintf( stdout, "Compressing simple bubbles...\n" );
- int n_compressed_bubbles;
- component->compress_all_bubbles( &n_compressed_bubbles, total_log_file, i+1, output_context );
+ int n_compressed_bubbles = 0;
+ component.compress_all_bubbles( &n_compressed_bubbles, total_log_file.get_ptr(), i+1, output_context );
fprintf( stdout, "Number of compressed bubbles: %d.\n", n_compressed_bubbles );
- int nbsnps = component->getNbOutput();
- if (nbsnps)
- fprintf(info_snp_file, "%d\t%d\n", i+1, nbsnps); // considering (i+1) and not i
-
+ int nbsnps = component.getNbOutput();
+ if (nbsnps) {
+ info_snp_file.fprintf("%d\t%d\n", i+1, nbsnps); // considering (i+1) and not i
+ }
// Recompress linear paths of size > 2
fprintf(stdout, "Recompressing linear paths...\n");
- original_size = (int)component->getNbNodes();
- component->compress_all_paths();
- fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - (int)component->getNbNodes() );
+ original_size = component.getNbNodes();
+ component.compress_all_paths();
+ fprintf( stdout, "Number of compressed nodes: %d.\n", original_size - component.getNbNodes() );
-
-
- if ( (int)component->getNbNodes() >= 4 )
- {
- ///////////////////////////
+ if (component.getNbNodes() >= 4) {
// IO optimization
- component->print_graph_edges_new( &lines_written_edges, contents_edge_file,total_edge_file[ii], NULL, NULL, false );
- component->print_graph_nodes_new( &lines_written_nodes, contents_node_file,total_node_file[ii], NULL, NULL, false );
- ///////////////////////////;
- }
- else {
- fprintf( contents_edge_file, "%d\n",lines_written_edges );
- fprintf( contents_node_file, "%d\n",lines_written_nodes );
+ component.print_graph_edges_new( &lines_written_edges, contents_edge_file.get_ptr(),current_total_edge_file.get_ptr(), NULL, NULL, false );
+ component.print_graph_nodes_new( &lines_written_nodes, contents_node_file.get_ptr(),current_total_node_file.get_ptr(), NULL, NULL, false );
+ } else {
+ contents_edge_file.fprintf("%d\n", lines_written_edges);
+ contents_node_file.fprintf("%d\n", lines_written_nodes);
}
- fprintf( stdout, "Final size: %d nodes.\n", (int)component->getNbNodes() );
- fprintf(info_file, "%d %d\n", i+1, (int)component->getNbNodes()); // outuput size of bcc for further use
- fprintf( stdout, "Done!\n\n" );
-
- ////////////////////////////
- ////////////////////////////
- ////////////////////////////
- // IO optimization (start)
- ////////////////////////////
- //check if file has to be changed - considering (i+1) and not i
- if ( ((i+1) % records_per_file == 0) && ((ii+1) < number_of_files_max) ) {
- ii++;
- sprintf( total_edge_fname, "%s_all_edges_bcc_%d", base_name.c_str(), ii+1 );
- total_edge_file[ii] = fopen(total_edge_fname,"w");
- sprintf( total_node_fname, "%s_all_nodes_bcc_%d", base_name.c_str(), ii+1 );
- total_node_file[ii] = fopen(total_node_fname, "w");
+ fprintf(stdout, "Final size: %d nodes.\n", component.getNbNodes());
+ info_file.fprintf("%d %d\n", i+1, component.getNbNodes()); // outuput size of bcc for further use
+ fprintf(stdout, "Done!\n\n");
+
+ // IO optimization: check if output bcc file has to be changed - considering (i+1) and not i
+ if (((i+1) % records_per_bcc_file == 0) && ((current_bcc_file_id+1) < output_bcc_file_count)) {
+ current_bcc_file_id += 1;
+ current_total_edge_file = File::open_path_sprintf("%s_all_edges_bcc_%d", "w", base_name, current_bcc_file_id+1);
+ current_total_node_file = File::open_path_sprintf("%s_all_nodes_bcc_%d", "w", base_name, current_bcc_file_id+1);
+
lines_written_edges = 0;
lines_written_nodes = 0;
//write an additional 0 in the first place
- fprintf( contents_edge_file, "%d\n",lines_written_edges );
- fprintf( contents_node_file, "%d\n",lines_written_nodes );
-
- //close the previous files, this avoids having too many open file at the smae time
- fclose(total_edge_file[ii-1]);
- fclose(total_node_file[ii-1]);
+ contents_edge_file.fprintf("%d\n", lines_written_edges);
+ contents_node_file.fprintf("%d\n", lines_written_nodes);
}
- ////////////////////////////
- // IO optimization (end)
- ////////////////////////////
- ////////////////////////////
- ////////////////////////////
-
- delete component;
}
- ///////////////////////////
- // IO optimization
- fclose(contents_edge_file);
- fclose(contents_node_file);
- fclose(total_log_file);
- fclose(info_snp_file);
- fclose(info_file);
- // Close just the last one
- fclose(total_edge_file[ii]);
- fclose(total_node_file[ii]);
-
- ///////////////////////////;
-
- // STL does not delete the objects in the vector when we call clear,
- // we have to do it manually !!!!!
- for ( vector<char*>::iterator it = seqs.begin() ; it != seqs.end() ; it++ )
- {
- delete [] *it;
- }
- seqs.clear();
+ for (char* seq : seqs) {
+ delete[] seq;
+ }
return EXIT_SUCCESS;
}
=====================================
tests/integration_tests/kisspliceDBGTest.py
=====================================
@@ -1,34 +1,53 @@
#!/usr/bin/env python3
-from sys import argv
-from os.path import dirname, abspath
-import filecmp
+import sys
+import os
import shutil
-import shlex
import subprocess
+import itertools
-TEST_INSTDIR = dirname(abspath(argv[0]))
-BINDIR = argv[1]
+TEST_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+BIN_DIR = sys.argv[1] # Provided by ctest call
result = subprocess.run(
- shlex.split(f"{BINDIR}/kissplice -k 25 -M 1000 -r {TEST_INSTDIR}/data/HBM75brain_100000.fasta -r {TEST_INSTDIR}/data/HBM75liver_100000.fasta --keep-counts -o {TEST_INSTDIR}/results"),
+ [
+ os.path.join(BIN_DIR, "kissplice"),
+ "-k", "25", "-M", "1000",
+ "-r", os.path.join(TEST_SCRIPT_DIR, "data", "HBM75brain_100000.fasta"),
+ "-r", os.path.join(TEST_SCRIPT_DIR, "data", "HBM75liver_100000.fasta"),
+ "--keep-counts",
+ "-o", os.path.join(TEST_SCRIPT_DIR, "results"),
+ ],
check = True, capture_output = True
)
assert result.stderr == b""
-# Extract entries at column_index, sort them and store them in file+"0"
-def copy_sorted_entries(column_index: int, file: str):
- with open(file) as lines:
- entries = [l.strip().split()[column_index] for l in lines]
- entries.sort()
- with open(file + "0", "w") as f:
- f.writelines(entry + "\n" for entry in entries)
+# Extract entries at column_index, sort them and compare to a reference in data/<filename>0 (pre-sorted)
+def compare_sorted_entries(filename: str, column_index: int):
+ # Extract column and sort entries of result
+ with open(os.path.join(TEST_SCRIPT_DIR, "results", filename)) as lines:
+ # Extract the column but restore the newline to have useful diffs
+ result_entries = [l.strip().split()[column_index] + "\n" for l in lines]
+ result_entries.sort()
+ with open(os.path.join(TEST_SCRIPT_DIR, "results", filename + "0"), "w") as f:
+ f.writelines(result_entries)
-copy_sorted_entries(2, f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.edges")
-copy_sorted_entries(1, f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.nodes")
-copy_sorted_entries(0, f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.abundance")
+ # On Linux these sorted entries are reproducible and exact.
+ # On MacOS they are almost the same, with one difference for 10k lines.
+ # Until this is investigated further, assume it is ok and add some tolerance to the test
+ diff_run = subprocess.run(
+ [
+ "diff",
+ os.path.join(TEST_SCRIPT_DIR, "data", filename + "0"),
+ os.path.join(TEST_SCRIPT_DIR, "result", filename + "0"),
+ ],
+ capture_output = True
+ )
+ diff_line_count = diff_run.stdout.count(ord("\n"))
+ allowed_lines_of_diff = 10
+ assert diff_line_count <= allowed_lines_of_diff # On error analyze the dumped files
-assert filecmp.cmp(f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.edges0", f"{TEST_INSTDIR}/data/graph_HBM75brain_100000_HBM75liver_100000_k25.edges0")
-assert filecmp.cmp(f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.nodes0", f"{TEST_INSTDIR}/data/graph_HBM75brain_100000_HBM75liver_100000_k25.nodes0")
-assert filecmp.cmp(f"{TEST_INSTDIR}/results/graph_HBM75brain_100000_HBM75liver_100000_k25.abundance0", f"{TEST_INSTDIR}/data/graph_HBM75brain_100000_HBM75liver_100000_k25.abundance0")
+compare_sorted_entries("graph_HBM75brain_100000_HBM75liver_100000_k25.edges", column_index = 2)
+compare_sorted_entries("graph_HBM75brain_100000_HBM75liver_100000_k25.nodes", column_index = 1)
+compare_sorted_entries("graph_HBM75brain_100000_HBM75liver_100000_k25.abundance", column_index = 0)
-shutil.rmtree(f"{TEST_INSTDIR}/results")
\ No newline at end of file
+shutil.rmtree(os.path.join(TEST_SCRIPT_DIR, "results"))
\ No newline at end of file
=====================================
thirdparty/kissreads/src/commons.cpp
=====================================
@@ -132,14 +132,14 @@ void * mycalloc(const int size, const int size_2){
void init_static_variables(const int k){
int i;
for (i=0;i<'T'+1;i++) comp[i]=i; // for other iupac alphabet letters
- comp['A']='T';
- comp['T']='A';
- comp['C']='G';
- comp['G']='C';
- comp['a']='t';
- comp['t']='a';
- comp['c']='g';
- comp['g']='c';
+ comp[static_cast<size_t>('A')]='T';
+ comp[static_cast<size_t>('T')]='A';
+ comp[static_cast<size_t>('C')]='G';
+ comp[static_cast<size_t>('G')]='C';
+ comp[static_cast<size_t>('a')]='t';
+ comp[static_cast<size_t>('t')]='a';
+ comp[static_cast<size_t>('c')]='g';
+ comp[static_cast<size_t>('g')]='c';
nuc[0]='A';
nuc[1]='C';
@@ -266,7 +266,7 @@ int get_next_sequence_and_comments_for_starters_fasta (char * sequence, char * c
//#endif
//printf("return sequence %s\n",sequence);
// free(line);
- return strlen(sequence); // readlen
+ return strlen(sequence); // readlen
}
@@ -301,7 +301,7 @@ int get_next_sequence_and_comments_for_starters_fastq (char * sequence, char * c
//#endif
//printf("return sequence %s\n",sequence);
// free(line);
- return strlen(sequence); // readlen
+ return strlen(sequence); // readlen
}
int get_next_sequence_and_comments_for_starters (char * sequence, char * comment, const char input_only_upper, char * line){
=====================================
thirdparty/kissreads/src/kissReads.cpp
=====================================
@@ -692,7 +692,7 @@ int main(int argc, char **argv) {
//4. Reverse the bubble if the left reads maps to the - strand
//The left reads must always map to the bubble in a forward way
//If they map in the RC of the bubble, we RC the sequence of the bubble, to force them map in a forward way
- char strandTheLeftReadsMapsTo;
+ char strandTheLeftReadsMapsTo = '\0';
if (leftReadFilesAgreedOnFW.size()>0) strandTheLeftReadsMapsTo = '+';
else if (leftReadFilesAgreedOnRC.size()>0) strandTheLeftReadsMapsTo = '-';
else if (rightReadFilesAgreedOnFW.size()>0) strandTheLeftReadsMapsTo = '-';
=====================================
thirdparty/kissreads/src/outputs.cpp
=====================================
@@ -48,7 +48,6 @@
#include <limits.h>
#include <math.h>
#define MAX(a,b) ((a) > (b) ? (a) : (b))
-#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define ABS(a) (((a) < 0) ? -(a) : (a))
//#define DEBUG_QUALITY
@@ -59,7 +58,6 @@
#endif
// Operation made on each data set (read_set_id)
-//#define op() MIN(corrected_avg_lo[read_set_id],corrected_avg_up[read_set_id]) / (corrected_avg_lo[read_set_id]+corrected_avg_up[read_set_id]);
#define op() corrected_avg_up[read_set_id] / (corrected_avg_lo[read_set_id]+corrected_avg_up[read_set_id]);
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/compare/a094828d0124c16f97d09787a230e8b5fa6fec17...e2f575018ee70f13794141b4e5155bef2954aebd
--
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/compare/a094828d0124c16f97d09787a230e8b5fa6fec17...e2f575018ee70f13794141b4e5155bef2954aebd
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