unit tests: fix compilation issues

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>

Ray-Technology-Research/MiSeq-Checkpoint.sh

@@ -10,6 +10,7 @@ mpiexec -n $NSLOTS \
 	-output-filename TestX \
 ./Ray -k 31 \
 -read-write-checkpoints save.ray \
+-debug \
 -write-seeds \
 -p \
 MiSeq_Ecoli_MG1655_110527_R1.fastq \

Ray-Technology-Research/MiSeq-mp2.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -N MiSeq-3
+#PBS -q qwork@mp2
+#PBS -l nodes=4:ppn=1
+#PBS -l walltime=1:00:00:00
+
+cd $PBS_O_WORKDIR
+
+module load openmpi_gcc64/1.6.4
+
+rm -rf TestX
+
+NSLOTS=96
+
+mpiexec -n $NSLOTS \
+	-output-filename TestX \
+./Ray -k 31 \
+-p \
+MiSeq_Ecoli_MG1655_110527_R1.fastq \
+MiSeq_Ecoli_MG1655_110527_R2.fastq \
+-write-kmers -write-seeds \
+-o TestX \

unit-tests/RayPlatform

@@ -0,0 +1 @@
+../RayPlatform

unit-tests/code

@@ -0,0 +1 @@
+ray/code

unit-tests/color_peak_quality_main.sh

@@ -1,5 +1,8 @@
 
-g++ color_peak_quality_main.cpp ../code/Searcher/QualityCaller.cpp -I . -I .. -I ../code  -o QualityCaller \
-../RayPlatform/core/statistics.cpp -I ../RayPlatform -DASSERT \
+g++ \
+color_peak_quality_main.cpp code/Searcher/QualityCaller.cpp -I .   -o QualityCaller \
+RayPlatform/core/statistics.cpp -DCONFIG_ASSERT \
+code/SequencesLoader/ReadHandle.cpp \
+code/SeedingData/PathHandle.cpp \
  -DCONFIG_CALLER_VERBOSE \
  -DCONFIG_CALLER_VERBOSE_POINTS

unit-tests/coverage_main.cpp

@@ -1,13 +1,16 @@
 #include <code/CoverageGatherer/CoverageDistribution.h>
+#include <code/Mock/constants.h>
+
+#include <unit-tests/unitTest.h>
+
 #include <string>
 #include <map>
-#include <unit-tests/unitTest.h>
 #include <fstream>
 #include <iostream>
+using namespace std;
+
 #include <stdint.h>
-#include <code/Mock/constants.h>
 #include <stdlib.h>
-using namespace std;
 
 int main(int argc,char**argv){
 	string file=argv[1];

unit-tests/graph_main.cpp

@@ -1,5 +1,7 @@
+
+#include <RayPlatform/routing/ConnectionGraph.h>
+
 #include <stdlib.h>
-#include <routing/ConnectionGraph.h>
 
 int main(int argc,char**argv){
 

unit-tests/graph_main.sh

@@ -1,16 +1,18 @@
 
-g++ -I ../RayPlatform -Wall \
+g++ -I . -Wall \
  -g \
 graph_main.cpp \
-../RayPlatform/routing/ConnectionGraph.cpp \
-../RayPlatform/core/statistics.cpp \
-../RayPlatform/routing/GraphImplementation.cpp \
-../RayPlatform/routing/GraphImplementationGroup.cpp \
-../RayPlatform/routing/GraphImplementationRandom.cpp \
-../RayPlatform/routing/GraphImplementationDeBruijn.cpp \
-../RayPlatform/routing/GraphImplementationKautz.cpp \
-../RayPlatform/routing/GraphImplementationExperimental.cpp \
-../RayPlatform/routing/GraphImplementationComplete.cpp \
+code/SeedingData/PathHandle.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+RayPlatform/routing/ConnectionGraph.cpp \
+RayPlatform/core/statistics.cpp \
+RayPlatform/routing/GraphImplementation.cpp \
+RayPlatform/routing/GraphImplementationGroup.cpp \
+RayPlatform/routing/GraphImplementationRandom.cpp \
+RayPlatform/routing/GraphImplementationDeBruijn.cpp \
+RayPlatform/routing/GraphImplementationKautz.cpp \
+RayPlatform/routing/GraphImplementationExperimental.cpp \
+RayPlatform/routing/GraphImplementationComplete.cpp \
 -o graph_main
 
 echo "Done compiling !"

unit-tests/main.sh

@@ -4,10 +4,6 @@
 
 source ../scripts/load-modules.sh
 
-export CODE=../code
-
-
-
 function getHandle(){
 	head /dev/urandom|sha1sum|awk '{print $1}'
 }

unit-tests/open-adressing.cpp

@@ -1,9 +1,11 @@
+
+#include <iostream>
+using namespace std;
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <stdint.h>
 #include <assert.h>
-#include <iostream>
-using namespace std;
 
 /**
  * make sure that double hashing can probe all the M buckets in M probing events

unit-tests/pagesize_main.cpp

@@ -1,3 +1,4 @@
+
 #include <unistd.h>
 #include <stdlib.h>
 #include <stdio.h>

unit-tests/peakFinder.cpp

@@ -1,4 +1,5 @@
-#include <Library/LibraryPeakFinder.h>
+#include <code/Library/LibraryPeakFinder.h>
+
 #include <fstream>
 #include <iostream>
 #include <vector>

unit-tests/ray

@@ -0,0 +1 @@
+../ray

unit-tests/scaffolder_test.cpp

@@ -1,6 +1,8 @@
-#include <Scaffolder/ScaffoldingAlgorithm.h>
-#include <Scaffolder/ScaffoldingVertex.h>
-#include <Scaffolder/ScaffoldingEdge.h>
+
+#include <code/Scaffolder/ScaffoldingAlgorithm.h>
+#include <code/Scaffolder/ScaffoldingVertex.h>
+#include <code/Scaffolder/ScaffoldingEdge.h>
+
 #include <string>
 #include <iostream>
 using namespace std;
@@ -42,7 +44,7 @@ int main(int argc,char**argv){
 	f2.close();
 	}
 
-	map<uint64_t,int> lengths;
+	map<PathHandle,int> lengths;
 
 	for(int i=0;i<(int)vertices.size();i++){
 		lengths[vertices[i].getName()]=vertices[i].getLength();
@@ -74,7 +76,7 @@ int main(int argc,char**argv){
 	solver.setVertices(&vertices);
 	solver.setEdges(&edges);
 
-	vector<vector<uint64_t> > m_scaffoldContigs;
+	vector<vector<PathHandle> > m_scaffoldContigs;
 	vector<vector<char> >m_scaffoldStrands;
 	vector<vector<int> >m_scaffoldGaps;
 

unit-tests/scaffolder_test.sh

@@ -1,10 +1,12 @@
 
 g++ scaffolder_test.cpp \
- ../code/Scaffolder/ScaffoldingVertex.cpp \
- ../code/Scaffolder/ScaffoldingEdge.cpp \
- ../code/Scaffolder/ScaffoldingAlgorithm.cpp \
- -O3 -o scaffolderTest -I ../code -I .. \
--I ../RayPlatform \
+code/SeedingData/PathHandle.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+code/Scaffolder/ScaffoldingVertex.cpp \
+code/Scaffolder/ScaffoldingEdge.cpp \
+code/Scaffolder/ScaffoldingAlgorithm.cpp \
+ -O3 -o scaffolderTest  \
+-I . \
 -Wall
 
 ./scaffolderTest vertices.txt edges.txt

unit-tests/sff_to_fasta_main.cpp

@@ -1,5 +1,6 @@
 #include <code/SequencesLoader/Loader.h>
 #include <code/SequencesLoader/Read.h>
+
 #include <stdint.h>
 #include <iostream>
 using namespace std;

unit-tests/test_alloc.cpp

@@ -1,4 +1,5 @@
-#include <MyAllocator.h>
+#include <RayPlatform/memory/MyAllocator.h>
+
 #include <iostream>
 using namespace std;
 

unit-tests/test_bz2reader_main.cpp

@@ -20,11 +20,13 @@
 
 */
 
-#include<stdlib.h>
-#include<iostream>
 #include<BzReader.h>
+
+#include<iostream>
 using namespace std;
 
+#include<stdlib.h>
+
 int main(){
 	BzReader reader;
 	reader.open((char*)"/data/users/sra/SRA001125/sdata/interleaved1.fastq.bz2");

unit-tests/test_bz_main.cpp

@@ -20,9 +20,9 @@
 
 */
 
-#include<stdlib.h>
-#include<iostream>
-#include<BzReader.h>
+#include <stdlib.h>
+#include <iostream>
+#include <BzReader.h>
 using namespace std;
 
 int main(){

unit-tests/test_coloredPeaks.cpp

@@ -1,9 +1,11 @@
+#include <code/Searcher/ColoredPeakFinder.h>
+
 #include <iostream>
-#include <Searcher/ColoredPeakFinder.h>
 #include <fstream>
 #include <vector>
 #include <assert.h>
 using namespace std;
+
 #include <unit-tests/unitTest.h>
 
 void run_test(string file,string result){

unit-tests/test_coloredPeaks.sh

@@ -1,5 +1,8 @@
 
-mpicxx  -g test_coloredPeaks.cpp ../code/Searcher/ColoredPeakFinder.cpp -I ../code/ -o test_coloredPeaks -I .. -I ../RayPlatform ../RayPlatform/core/statistics.cpp
+mpicxx \
+code/SeedingData/PathHandle.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+-g test_coloredPeaks.cpp code/Searcher/ColoredPeakFinder.cpp -I. -o test_coloredPeaks RayPlatform/core/statistics.cpp
 
 prog=$(pwd)/test_coloredPeaks
 

unit-tests/test_coverage_distribution.sh

@@ -1,5 +1,7 @@
-g++ coverage_main.cpp ../code/CoverageGatherer/CoverageDistribution.cpp -O3 -o CoverageExe -I ../code -I .. \
--I ../RayPlatform
+g++ \
+code/SeedingData/PathHandle.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+coverage_main.cpp code/CoverageGatherer/CoverageDistribution.cpp -O3 -o CoverageExe -I . 
 
 for i in $(ls CoverageDistribution/*.expected)
 do

unit-tests/test_getEdges.cpp

@@ -1,11 +1,14 @@
-#include <unitTest.h>
-#include <Kmer.h>
-#include <common_functions.h>
-#include <assert.h>
+#include <unit-tests/unitTest.h>
+
+#include <code/KmerAcademyBuilder/Kmer.h>
+#include <code/Mock/common_functions.h>
+
 #include <string>
 #include <iostream>
 using namespace std;
 
+#include <assert.h>
+
 int main(int argc,char**argv){
 
 	return 0;

unit-tests/test_getedges.sh

@@ -1,9 +1,12 @@
 
 mpicxx -g \
- ../RayPlatform/*/*.cpp \
-../code/SeedingData/GraphPath.cpp \
-../code/SeedExtender/Direction.cpp ../code/VerticesExtractor/Vertex.cpp ../code/SequencesIndexer/ReadAnnotation.cpp \
- test_kmer.cpp ../code/Mock/common_functions.cpp ../code/KmerAcademyBuilder/Kmer.cpp \
- -I. -D MAXKMERLENGTH=32 -DASSERT -I../code -I ../RayPlatform -I ..
+RayPlatform/*/*.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+code/SeedingData/PathHandle.cpp \
+code/SeedingData/GraphPath.cpp \
+code/SeedExtender/Direction.cpp code/VerticesExtractor/Vertex.cpp code/SequencesIndexer/ReadAnnotation.cpp \
+ test_kmer.cpp code/Mock/common_functions.cpp code/KmerAcademyBuilder/Kmer.cpp \
+ -I. -D CONFIG_MAXKMERLENGTH=32 -DCONFIG_ASSERT 
+
 ./a.out TGAAATGGAAATGGTCTGGGACG
 

unit-tests/test_grid.cpp

@@ -1,6 +1,7 @@
-#include <graph/GridTable.h>
+#include <code/graph/GridTable.h>
+#include <code/graph/GridTableIterator.h>
+
 #include <iostream>
-#include <graph/GridTableIterator.h>
 using namespace std;
 
 int main(){

unit-tests/test_invert.cpp

@@ -1,9 +1,12 @@
-#include <unit-tests/unitTest.h>
 #include <code/Mock/common_functions.h>
-#include <stdint.h>
+
+#include <unit-tests/unitTest.h>
+
 #include <iostream>
 using namespace std;
 
+#include <stdint.h>
+
 /** invertEdges was removed */
 int main(){
 	return 0;

unit-tests/test_invert.sh

@@ -1,7 +1,9 @@
 mpicxx \
-../RayPlatform/*/*.cpp \
-../code/SeedingData/GraphPath.cpp \
- -I../code ../code/Mock/common_functions.cpp test_invert.cpp -g -DMAXKMERLENGTH=32 \
-../code/KmerAcademyBuilder/Kmer.cpp  -I .. -I ../RayPlatform
+RayPlatform/*/*.cpp \
+code/SeedingData/PathHandle.cpp \
+code/SequencesLoader/ReadHandle.cpp \
+code/SeedingData/GraphPath.cpp \
+code/Mock/common_functions.cpp test_invert.cpp -g -DCONFIG_MAXKMERLENGTH=32 \
+code/KmerAcademyBuilder/Kmer.cpp  -I .
 
 ./a.out