Skip to content

Commit

Permalink
Tidied CMakeLists.txt and src/modules/hbv2gfa.cc
Browse files Browse the repository at this point in the history
  • Loading branch information
Jon Wright committed Sep 12, 2016
1 parent 696839e commit 021df32
Show file tree
Hide file tree
Showing 2 changed files with 176 additions and 30 deletions.
168 changes: 157 additions & 11 deletions CMakeLists.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -163,9 +163,7 @@ add_library(base_libs OBJECT
src/system/file/FileReader.cc
src/system/file/FileWriter.cc
src/system/file/TempFile.cc
src/util/Logger.cc)

add_library(base2_libs OBJECT
src/util/Logger.cc
src/fastg/FastgGraph.cc
src/graphics/BasicGraphics.cc
src/kmers/kmer_parcels/KmerParcelsBuilder.cc
Expand All @@ -176,7 +174,6 @@ add_library(base2_libs OBJECT
src/paths/MakeAlignsPathsParallelX.cc
src/paths/ReadsToPathsCoreX.cc
src/paths/RemodelGapTools.cc
src/paths/RemodelGapTools.cc
src/paths/UnibaseUtils.cc
src/paths/Unipath.cc
src/paths/long/AssessBestAlignCore.cc
Expand Down Expand Up @@ -213,6 +210,158 @@ add_library(base2_libs OBJECT
src/random/NormalDistribution.cc
src/util/TextTable.cc)

add_library(hb_base_libs OBJECT
src/Alignment.cc
src/BlockAlign.cc
src/Charvector.cc
src/Equiv.cc
src/FastIfstream.cc
src/Fastavector.cc
src/Floatvector.cc
src/IndexedAlignmentPlusVector.cc
src/IntPairVec.cc
src/Intvector.cc
src/LinkTimestamp.cc
src/MemberOf.cc
src/PackAlign.cc
src/PairsManager.cc
src/ParseRange.cc
src/ParseSet.cc
src/PrintAlignment.cc
src/Qualvector.cc
src/ScoreAlignment.cc
src/Superb.cc
src/TokenizeString.cc
src/Vec.cc
src/VecAlignmentPlus.cc
src/dna/Bases.cc
src/efasta/AmbiguityScore.cc
src/efasta/EfastaTools.cc
src/feudal/BaseVec.cc
src/feudal/BinaryStream.cc
src/feudal/BitVec.cc
src/feudal/CharString.cc
src/feudal/FeudalControlBlock.cc
src/feudal/FeudalFileReader.cc
src/feudal/FeudalFileWriter.cc
src/feudal/FeudalTools.cc
src/feudal/FieldVec.cc
src/feudal/Generic.cc
src/feudal/Mempool.cc
src/feudal/Oob.cc
src/feudal/PQVec.cc
src/graph/Digraph.cc
src/graph/FindCells.cc
src/kmers/BigKPather.cc
src/kmers/KMerContext.cc
src/kmers/KmerRecord.cc
src/kmers/ReadPather.cc
src/lookup/LookAlign.cc
src/lookup/SAM.cc
src/lookup/SAM2CRD.cc
src/math/Functions.cc
src/math/HoInterval.cc
src/math/Matrix.cc
src/math/Permutation.cc
src/math/PowerOf2.cc
src/pairwise_aligners/ClusterAligner.cc
src/pairwise_aligners/SmithWatBandedA.cc
src/pairwise_aligners/SmithWatFree.cc
src/paths/BigMapTools.cc
src/paths/FindErrorsCore.cc
src/paths/HyperBasevector.cc
src/paths/HyperEfasta.cc
src/paths/KmerBaseBroker.cc
src/paths/KmerPath.cc
src/paths/KmerPathInterval.cc
src/paths/LongReadTools.cc
src/paths/MergeReadSetsCore.cc
src/paths/ProcessGap.cc
src/paths/Sepdev.cc
src/paths/UnipathScaffold.cc
src/paths/Uniseq.cc
src/paths/long/Correct1.cc
src/paths/long/Correct1Pre.cc
src/paths/long/CorrectByStack.cc
src/paths/long/CorrectPairs1.cc
src/paths/long/DiscovarTools.cc
src/paths/long/EMEC3.cc
src/paths/long/FillPairs.cc
src/paths/long/FriendAligns.cc
src/paths/long/HBVFromEdges.cc
src/paths/long/LargeKDispatcher.cc
src/paths/long/LoadCorrectCore.cc
src/paths/long/LongProtoTools.cc
src/paths/long/LongReadsToPaths.cc
src/paths/long/MakeAlignments.cc
src/paths/long/PreCorrectAlt1.cc
src/paths/long/PreCorrectOldNew.cc
src/paths/long/ReadPathTools.cc
src/paths/long/ReadStack.cc
src/random/Bernoulli.cc
src/random/RNGen.cc
src/reporting/PerfStat.cc
src/system/Assert.cc
src/system/ErrNo.cc
src/system/Exit.cc
src/system/HostName.cc
src/system/ParsedArgs.cc
src/system/ProcBuf.cc
src/system/SysConf.cc
src/system/System.cc
src/system/Thread.cc
src/system/ThreadsafeIO.cc
src/system/TraceVal.cc
src/system/UseGDB.cc
src/system/WorklistUtils.cc
src/system/file/File.cc
src/system/file/FileReader.cc
src/system/file/FileWriter.cc
src/system/file/TempFile.cc
src/util/Logger.cc
src/fastg/FastgGraph.cc
src/graphics/BasicGraphics.cc
src/kmers/kmer_parcels/KmerParcelsBuilder.cc
src/math/IntDistribution.cc
src/pairwise_aligners/MaxMutmerFromMer.cc
src/pairwise_aligners/SmithWatAffine.cc
src/paths/MakeAlignsPathsParallelX.cc
src/paths/ReadsToPathsCoreX.cc
src/paths/RemodelGapTools.cc
src/paths/UnibaseUtils.cc
src/paths/Unipath.cc
src/paths/long/AssessBestAlignCore.cc
src/paths/long/CleanEfasta.cc
src/paths/long/CreateGenome.cc
src/paths/long/DigraphFromWords.cc
src/paths/long/EvalByReads.cc
src/paths/long/KmerCount.cc
src/paths/long/LongHyper.cc
src/paths/long/ReadOriginTracker.cc
src/paths/long/RefTrace.cc
src/paths/long/RefTraceControl.cc
src/paths/long/RefTraceTools.cc
src/paths/long/SupportedHyperBasevector.cc
src/paths/long/SupportedHyperBasevector3.cc
src/paths/long/SupportedHyperBasevector4.cc
src/paths/long/SupportedHyperBasevector5.cc
src/paths/long/SupportedHyperBasevector6.cc
src/paths/long/SupportedHyperBasevector7.cc
src/paths/long/VariantCallTools.cc
src/paths/long/VariantFilters.cc
src/paths/long/VariantPostProcess.cc
src/paths/long/VariantReadSupport.cc
src/paths/long/Variants.cc
src/paths/long/large/CN1PeakFinder.cc
src/paths/long/large/GapToyTools.cc
src/paths/long/large/GapToyTools3.cc
src/paths/long/large/Lines.cc
src/paths/long/large/LocalLayout.cc
src/paths/simulation/VCF.cc
src/random/NormalDistribution.cc
src/util/TextTable.cc
src/GFADump.cc)

add_library(specific_w2rap-contigger OBJECT
src/AnnotatedContig.cc
src/BasevectorTools.cc
Expand Down Expand Up @@ -249,21 +398,18 @@ add_library(specific_w2rap-contigger OBJECT
src/paths/long/large/tools/NhoodInfoCore.cc
src/paths/long/large/tools/NhoodInfoState.cc
src/paths/long/large/tools/NhoodInfoStuff.cc
src/GFADump.cc src/paths/PathFinder.cc src/paths/PathFinder.h)

src/GFADump.cc
src/paths/PathFinder.cc
src/paths/PathFinder.h)

## add executables and respective sources
add_executable(w2rap-contigger src/modules/w2rap-contigger.cc
$<TARGET_OBJECTS:specific_w2rap-contigger>
$<TARGET_OBJECTS:base_libs>
$<TARGET_OBJECTS:base2_libs>
)

add_executable(hbv2gfa src/modules/hbv2gfa.cc
$<TARGET_OBJECTS:specific_w2rap-contigger>
$<TARGET_OBJECTS:base_libs>
$<TARGET_OBJECTS:base2_libs>

$<TARGET_OBJECTS:hb_base_libs>
)

##Zlib link
Expand Down
38 changes: 19 additions & 19 deletions src/modules/hbv2gfa.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,30 +2,30 @@
// Created by Bernardo Clavijo (TGAC) on 21/06/2016.
//
#include <paths/long/large/Repath.h>
#include <paths/long/large/Clean200.h>
#include <paths/long/large/Simplify.h>
#include <paths/long/large/MakeGaps.h>
//#include <paths/long/large/Clean200.h>
//#include <paths/long/large/Simplify.h>
//#include <paths/long/large/MakeGaps.h>
#include <paths/long/large/FinalFiles.h>
#include "FastIfstream.h"
#include "FetchReads.h"
#include "MainTools.h"
#include "PairsManager.h"
//#include "FastIfstream.h"
//#include "FetchReads.h"
//#include "MainTools.h"
//#include "PairsManager.h"
#include "ParallelVecUtilities.h"
#include "feudal/PQVec.h"
//#include "feudal/PQVec.h"
#include "lookup/LookAlign.h"
#include "paths/HyperBasevector.h"
#include "paths/RemodelGapTools.h"
#include "paths/long/BuildReadQGraph.h"
//#include "paths/HyperBasevector.h"
//#include "paths/RemodelGapTools.h"
//#include "paths/long/BuildReadQGraph.h"
//#include "paths/long/PlaceReads0.h"
#include "paths/long/SupportedHyperBasevector.h"
#include "paths/long/large/AssembleGaps.h"
#include "paths/long/large/ExtractReads.h"
//#include "paths/long/SupportedHyperBasevector.h"
//#include "paths/long/large/AssembleGaps.h"
//#include "paths/long/large/ExtractReads.h"
#include "tclap/CmdLine.h"
#include <sys/types.h>
#include <sys/stat.h>
#include <time.h>
#include <sys/time.h>
#include <paths/PathFinder.h>
//#include <sys/types.h>
//#include <sys/stat.h>
//#include <time.h>
//#include <sys/time.h>
//#include <paths/PathFinder.h>
#include "GFADump.h"

int main(const int argc, const char * argv[]) {
Expand Down

0 comments on commit 021df32

Please sign in to comment.