bio-velvet_underground 0.2.0 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 696cf2a0e11ae0c6848fe4d717e1add4e1452370
-  data.tar.gz: 3b88bb295352c038eddeb118835e88596b66641b
+  metadata.gz: 65689e857131512e65603fb6fa5f6d66cca0b9af
+  data.tar.gz: f3898e399d3ff7c44e6ebcb37920be2a119603e2
 SHA512:
-  metadata.gz: 464490f17d6ab3a98c47c4a4fe7f7dcd08359ba02284986a45119106d8a29da620c1417c1af0d1615199fc912adb0331fdf66242968f5b63f8e2cc03cdf4e1f2
-  data.tar.gz: a0331bd42caecc5adbb2fde466e2c8ea6de71db07c621f844a8ccc9456e78ef13ea1ce41073052bd574e32655676c057d3854a44c9875bedad1314c322746345
+  metadata.gz: 86af06bc883460bd7c05d3f3a3925cd9e9aaf7b2914d552936a84ad243c322f4777b0797c58c868a3f7045507a969a2d2b1f1b2ad56f593d4ab3a011afab2b6a
+  data.tar.gz: 4e42bf15c4bfde9bdd437203b2f559caef66fd3c47c86cabd5f6255f1666c4933e6253b7ae09f21622748f25dc4b495cee77e90b035b7edcc24f2cc2c16ae2f6

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/ext/src/Makefile

@@ -20,14 +20,14 @@ endif
 
 ifdef VBIGASSEMBLY
 override DEF := $(DEF) -D BIGASSEMBLY -D VBIGASSEMBLY
-endif 	
+endif
 
 
 ifdef LONGSEQUENCES
 override DEF := $(DEF) -D LONGSEQUENCES
 endif
 
-# OpenMP 
+# OpenMP
 ifdef OPENMP
 override CFLAGS := $(CFLAGS) -fopenmp
 endif
@@ -39,23 +39,24 @@ endif
 
 OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/scaffold.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o
 OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+OBJSHARED = $(subst obj,obj/shared,$(OBJ))
 
-default : cleanobj zlib obj velveth velvetg doc
+default : zlib obj velveth velvetg
 
 clean : clean-zlib
-	-rm obj/*.o obj/dbg/*.o ./velvet* 
+	-rm obj/*.o obj/dbg/*.o obj/shared/*.o obj/shared/velvet.so.0.0.1 ./velvet*
 	-rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log
 	-rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log
 
-cleanobj: 
-	-rm obj/*.o obj/dbg/*.o 
+cleanobj:
+	-rm obj/*.o obj/dbg/*.o obj/shared/*.o
 
 ifdef BUNDLEDZLIB
 Z_LIB_DIR=third-party/zlib-1.2.3
 Z_LIB_FILES=$(Z_LIB_DIR)/*.o
 override DEF := $(DEF) -D BUNDLEDZLIB
 
-zlib: 
+zlib:
 	cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
 
 clean-zlib :
@@ -67,14 +68,14 @@ zlib :
 clean-zlib :
 endif
 
-velveth : obj 
+velveth : obj
 	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
 
 
 velvetg : obj
 	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o $(Z_LIB_FILES) $(LIBS)
 
-debug : override DEF := $(DEF) -D DEBUG 
+debug : override DEF := $(DEF) -D DEBUG
 debug : cleanobj obj/dbg
 	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
 	$(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/binarySequences.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o obj/dbg/autoOpen.o $(Z_LIB_FILES) $(LIBS)
@@ -92,25 +93,25 @@ colordebug : cleanobj obj/dbg_de
 objdir:
 	mkdir -p obj
 
-obj: zlib cleanobj objdir $(OBJ)
+obj: zlib objdir $(OBJ)
 
 obj_de: override DEF := $(DEF) -D COLOR
 obj_de: zlib cleanobj objdir $(OBJ)
 
-obj/dbgdir: 
+obj/dbgdir:
 	mkdir -p obj/dbg
 
-obj/dbg: override DEF := $(DEF) -D DEBUG 
+obj/dbg: override DEF := $(DEF) -D DEBUG
 obj/dbg: zlib cleanobj obj/dbgdir $(OBJDBG)
 
 obj/dbg_de: override DEF := $(DEF) -D COLOR -D DEBUG
 obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG)
 
 obj/%.o: src/%.c
-	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ 
+	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
 
 obj/dbg/%.o: src/%.c
-	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ 
+	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
 
 doc: Manual.pdf
 
@@ -123,3 +124,15 @@ endif
 
 test: velvetg velveth
 	cd tests && ./run-tests.sh
+
+sharedobjdir:
+	mkdir -p obj/shared
+
+obj/shared: sharedobjdir $(OBJSHARED)
+
+obj/shared/%.o: src/%.c
+	$(CC) -fPIC $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@
+
+shared: zlib obj/shared
+	cd obj/shared && gcc -shared -Wl,-soname,libvelvet.so.1 -o libvelvet.so.1.0 allocArray.o autoOpen.o binarySequences.o concatenatedGraph.o concatenatedPreGraph.o correctedGraph.o dfibHeap.o dfib.o fibHeap.o fib.o graph.o graphReConstruction.o graphStats.o kmer.o kmerOccurenceTable.o locallyCorrectedGraph.o passageMarker.o preGraphConstruction.o preGraph.o readCoherentGraph.o readSet.o recycleBin.o roadMap.o scaffold.o shortReadPairs.o splay.o splayTable.o tightString.o utility.o run.o run2.o
+

data/ext/src/src/concatenatedPreGraph.c

@@ -47,7 +47,7 @@ static void concatenatePreNodes(IDnum preNodeAID, PreArcI oldPreArc,
 		       hasSinglePreArc_pg(getOtherEnd_pg
 					  (preArc, preNodeBID),
 					  preGraph)
-		       && !isLoop_pg(preArc) 
+		       && !isLoop_pg(preArc)
 		       && getDestination_pg(preArc, preNodeBID) != preNodeAID) {
 
 		totalLength += getPreNodeLength_pg(preNodeBID, preGraph);
@@ -99,11 +99,11 @@ static void concatenatePreNodes(IDnum preNodeAID, PreArcI oldPreArc,
 		appendDescriptors_pg(&ptr, &writeOffset ,currentPreNodeID, preGraph, false);
 	}
 
-	if (writeOffset != 0) 
+	if (writeOffset != 0)
 		while (writeOffset++ != 4)
 			(*ptr) >>= 2;
 
-	setPreNodeDescriptor_pg(descr, totalLength - wordLength + 1, preNodeAID, preGraph); 
+	setPreNodeDescriptor_pg(descr, totalLength - wordLength + 1, preNodeAID, preGraph);
 
 	// Correct preArcs
 	for (preArc = getPreArc_pg(preNodeBID, preGraph); preArc != NULL_IDX;
@@ -209,7 +209,7 @@ static boolean isEligibleTip(IDnum index, PreGraph * preGraph, Coordinate
 	if (currentIndex == 0)
 		return true;
 
-	// Joined tips  
+	// Joined tips
 	if (simplePreArcCount_pg(-currentIndex, preGraph) < 2)
 		return false;
 

data/ext/src/src/correctedGraph.c

@@ -764,7 +764,7 @@ static void remapNodeMarkersOntoNeighbour(Node * source,
 		}
 	}
 
-	// Short read markers 
+	// Short read markers
 	if (readStartsAreActivated(graph)) {
 		// Update Coordinates
 		sourceArray = getNodeReads(source, graph);
@@ -1250,7 +1250,7 @@ static void foldSymmetricalNode(Node * node)
 		twinNode = node;
 		node = tmp;
 	}
-	// Destroy link to old markers 
+	// Destroy link to old markers
 	setMarker(node, NULL_IDX);
 
 	// Reinsert markers properly
@@ -1951,7 +1951,7 @@ static void transferNodeData(Node * source, Node * target)
 	if (getNode(fastPath) == twinSource)
 		fastPath = getNextInSequence(fastPath);
 
-	// Next node 
+	// Next node
 	if (source == activeNode) {
 		activeNode = target;
 		todo =
@@ -2013,7 +2013,7 @@ static void concatenateNodesAndVaccinate(Node * nodeA, Node * nodeB,
 	// Read starts
 	concatenateReadStarts(nodeA, nodeB, graph);
 
-	// Descriptor management 
+	// Descriptor management
 	appendDescriptors(nodeA, nodeB);
 
 	// Update uniqueness:
@@ -2167,7 +2167,7 @@ static void cleanUpRedundancy()
 
 	//velvetLog("Concatenation\n");
 
-	// Freeing up memory  
+	// Freeing up memory
 	if (slowMarker != NULL_IDX)
 		concatenatePathNodes(slowPath);
 	else
@@ -2460,7 +2460,7 @@ void clipTipsHard(Graph * graph, boolean conserveLong)
 
 			if (current == NULL)
 				continue;
-	
+
 			if (conserveLong && getMarker(current))
 				continue;
 
@@ -2560,7 +2560,7 @@ void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category *
 	eligibleStartingPoints = mallocOrExit(2 * nodes + 1, IDnum);
 	progressStatus = callocOrExit(2 * nodes + 1, boolean);
 	todoLists = callocOrExit(2 * nodes + 1, Ticket *);
-	//Done with memory 
+	//Done with memory
 
 	resetNodeStatus(graph);
 	determineEligibleStartingPoints();
@@ -2607,9 +2607,9 @@ void setMaxReadLength(int value)
 	if (value < 0) {
 		velvetLog("Negative branch length %i!\n", value);
 		velvetLog("Exiting...\n");
-#ifdef DEBUG 
+#ifdef DEBUG
 		abort();
-#endif 
+#endif
 		exit(1);
 	}
 	MAXREADLENGTH = value;
@@ -2621,9 +2621,9 @@ void setMaxGaps(int value)
 	if (value < 0) {
 		velvetLog("Negative max gap count %i!\n", value);
 		velvetLog("Exiting...\n");
-#ifdef DEBUG 
+#ifdef DEBUG
 		abort();
-#endif 
+#endif
 		exit(1);
 	}
 	MAXGAPS = value;
@@ -2635,9 +2635,9 @@ void setMaxDivergence(double value)
 		velvetLog("Divergence rate %lf out of bounds [0,1]!\n",
 		       value);
 		velvetLog("Exiting...\n");
-#ifdef DEBUG 
+#ifdef DEBUG
 		abort();
-#endif 
+#endif
 		exit(1);
 	}
 	MAXDIVERGENCE = value;

data/ext/src/src/graphStats.c

@@ -522,7 +522,7 @@ void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads)
 		}
 
 		velvetFprintf(outfile, "\t%li", (long) markerCount(node));
-		printShortCounts(outfile, node, graph, reads); 
+		printShortCounts(outfile, node, graph, reads);
 
 		velvetFprintf(outfile, "\n");
 	}
@@ -579,7 +579,7 @@ void displayLocalBreakpoint(PassageMarkerI strainMarker,
 	if (destination == NULL)
 		return;
 
-	// Eliminate those that point to uniquely strain sequences 
+	// Eliminate those that point to uniquely strain sequences
 	if (nodeGenomicMultiplicity(destination, firstStrain) != 1) {
 //              velvetLog("Multiple genome reads\n");
 		return;
@@ -600,7 +600,7 @@ void displayLocalBreakpoint(PassageMarkerI strainMarker,
 	if (destination == destination2)
 		return;
 
-	// Eliminate those that point to uniquely strain sequences 
+	// Eliminate those that point to uniquely strain sequences
 	if (isOnlyGenome(destination2, firstStrain))
 		return;
 
@@ -776,7 +776,7 @@ static Mask * lowCoverageRegions(Coordinate * starts, Coordinate * stops, size_t
 				if (regions) {
 					lastRegion->next = newMask(stops[indexStop]);
 					lastRegion = lastRegion->next;
-				} else { 
+				} else {
 					regions = newMask(stops[indexStop]);
 					lastRegion = regions;
 				}
@@ -803,7 +803,7 @@ static Mask * lowCoverageRegions(Coordinate * starts, Coordinate * stops, size_t
 			if (regions) {
 				lastRegion->next = newMask(stops[indexStop]);
 				lastRegion = lastRegion->next;
-			} else { 
+			} else {
 				regions = newMask(stops[indexStop]);
 				lastRegion = regions;
 			}
@@ -837,7 +837,7 @@ static int compareCoords(const void * A, const void * B) {
 
 static void sortCoords(Coordinate * array, IDnum length) {
 	qsort(array, (size_t) length, sizeof(Coordinate), compareCoords);
-} 
+}
 
 static void getShortReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths) {
 	ShortReadMarker * markers = getNodeReads(node, graph);
@@ -918,7 +918,7 @@ static void exportLongNodeSequence(FILE * outfile, Node * node, Graph * graph, R
 	gap = getGap(node, graph);
 	for (position = 0; position < WORDLENGTH; position++) {
 		if (position % 60 == 0 && position > 0)
-			velvetFprintf(outfile, "\n"); 
+			velvetFprintf(outfile, "\n");
 		nucleotide = getNucleotideChar(position, tString);
 		velvetFprintf(outfile, "%c", nucleotide);
 	}
@@ -938,7 +938,7 @@ static void exportLongNodeSequence(FILE * outfile, Node * node, Graph * graph, R
 		    mask->finish) {
 			next = mask->next;
 			deallocateMask(mask);
-			mask = next;	
+			mask = next;
 		}
 
 		if (gap
@@ -1047,7 +1047,7 @@ int compareNodeCovs(const void * A, const void * B) {
 	Node * nodeB = *((Node **) B);
 	double covA;
 	double covB;
-	
+
 	if (getNodeLength(nodeA) == 0)
 		nodeA = NULL;
 
@@ -1063,8 +1063,8 @@ int compareNodeCovs(const void * A, const void * B) {
 		return -1;
 
 	// Deal with real coverage numbers:
-	covA = getTotalCoverage(nodeA) / (double) getNodeLength(nodeA);	
-	covB = getTotalCoverage(nodeB) / (double) getNodeLength(nodeB);	
+	covA = getTotalCoverage(nodeA) / (double) getNodeLength(nodeA);
+	covB = getTotalCoverage(nodeB) / (double) getNodeLength(nodeB);
 
 	if (covA > covB)
 		return 1;
@@ -1075,14 +1075,14 @@ int compareNodeCovs(const void * A, const void * B) {
 
 double estimated_cov(Graph * graph, char * directory)
 {
-	Node ** nodeArray = callocOrExit(nodeCount(graph), Node*); 
+	Node ** nodeArray = callocOrExit(nodeCount(graph), Node*);
 	IDnum index;
 	Coordinate halfTotalLength = 0;
 	Coordinate sumLength = 0;
 	Node *node;
 	char *logFilename =
 	    mallocOrExit(strlen(directory) + 100, char);
-	char *statsLine = 
+	char *statsLine =
 	    mallocOrExit(5000, char);
 	FILE *logFile;
 
@@ -1152,7 +1152,7 @@ static boolean terminalReferenceMarker(Node * node, ReadSet * reads) {
 
 static boolean hasReferenceMarker(Node * node, ReadSet * reads) {
 	PassageMarkerI marker;
-	
+
 	for (marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker))
 		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] == REFERENCE)
 			return true;
@@ -1229,14 +1229,14 @@ boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
 	IDnum index;
 	Node *node;
 	boolean denounceReads = readStartsAreActivated(graph);
-	boolean *res = NULL; 
+	boolean *res = NULL;
 	FILE * outfile = NULL;
 
 	velvetLog("Removing contigs with coverage < %f...\n", minCov);
-		
+
 	if (denounceReads)
 		res = callocOrExit(sequenceCount(graph), boolean);
-		
+
 	if (export) {
 		outfile = fopen(filename, "w");
 
@@ -1255,7 +1255,7 @@ boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
 		if (getNodeLength(node) == 0)
 			continue;
 
-		if (getTotalCoverage(node) / getNodeLength(node) < minCov 
+		if (getTotalCoverage(node) / getNodeLength(node) < minCov
 		    && !hasReferenceMarker(node, reads))
 			removeNodeAndDenounceDubiousReads(graph,
 							  node,
@@ -1273,7 +1273,7 @@ boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
 		if (getNodeLength(node) == 0)
 			continue;
 
-		if (getTotalCoverage(node) / getNodeLength(node) < minCov 
+		if (getTotalCoverage(node) / getNodeLength(node) < minCov
 		    && !terminalReferenceMarker(node, reads))
 			removeNodeAndDenounceDubiousReads(graph,
 							  node,
@@ -1296,7 +1296,7 @@ static Coordinate getLongCoverage(Node * node) {
 
 	for (marker = getMarker(node); marker; marker = getNextInNode(marker))
 		total += getPassageMarkerLength(marker);
-	
+
 	return total;
 }
 
@@ -1313,7 +1313,7 @@ void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLon
 		if (getNodeLength(node) == 0)
 			continue;
 
-		if ((getTotalCoverage(node) / getNodeLength(node) < minCov 
+		if ((getTotalCoverage(node) / getNodeLength(node) < minCov
 		    || getLongCoverage(node) / getNodeLength(node) < minLongCov)
 		    && hasReferenceMarker(node, reads)) {
 			destroyNodePassageMarkers(graph, node);
@@ -1342,7 +1342,7 @@ void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
 		return;
 
 	velvetLog("Removing contigs with coverage < %f...\n", minCov);
-		
+
 	if (export) {
 		outfile = fopen(filename, "a");
 
@@ -1360,7 +1360,7 @@ void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
 		if (getNodeLength(node) == 0)
 			continue;
 
-		if (getLongCoverage(node) / getNodeLength(node) < minCov 
+		if (getLongCoverage(node) / getNodeLength(node) < minCov
 		    && !hasReferenceMarker(node, reads))
 			removeNodeAndDenounceDubiousReads(graph,
 							  node,
@@ -1378,7 +1378,7 @@ void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
 		if (getNodeLength(node) == 0)
 			continue;
 
-		if (getLongCoverage(node) / getNodeLength(node) < minCov 
+		if (getLongCoverage(node) / getNodeLength(node) < minCov
 		    && !terminalReferenceMarker(node, reads))
 			removeNodeAndDenounceDubiousReads(graph,
 							  node,
@@ -1404,7 +1404,7 @@ void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coord
 		return;
 
 	velvetLog("Applying an upper coverage cutoff of %f...\n", maxCov);
-		
+
 	if (export) {
 		outfile = fopen(filename, "w");
 
@@ -1423,7 +1423,7 @@ void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coord
 		    && getTotalCoverage(node) / getNodeLength(node) > maxCov) {
 			destroyNodePassageMarkers(graph, node);
 
-			if (export && getNodeLength(node) > minLength) 
+			if (export && getNodeLength(node) > minLength)
 				exportLongNodeSequence(outfile, node, graph, NULL, NULL, -1);
 
 			destroyNode(node, graph);
@@ -1784,7 +1784,7 @@ Coordinate totalAssemblyLength(Graph * graph)
 	return total;
 }
 
-IDnum usedReads(Graph * graph, Coordinate minContigLength) 
+IDnum usedReads(Graph * graph, Coordinate minContigLength)
 {
 	IDnum res = 0;
 	boolean * used = callocOrExit(sequenceCount(graph) + 1, boolean);
@@ -1798,16 +1798,16 @@ IDnum usedReads(Graph * graph, Coordinate minContigLength)
 		node = getNodeInGraph(graph, nodeID);
 		if (node == NULL || getNodeLength(node) < minContigLength)
 			continue;
-		
+
 		// Long reads
 		for(marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker)) {
 			readID = getPassageMarkerSequenceID(marker);
 			if (readID < 0)
 				readID = -readID;
-			used[readID] = true;	
-		}	
+			used[readID] = true;
+		}
 
-		// Short reads		
+		// Short reads
 		if (!readStartsAreActivated(graph))
 			continue;
 
@@ -1816,23 +1816,23 @@ IDnum usedReads(Graph * graph, Coordinate minContigLength)
 		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
 			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
 			readID = getShortReadMarkerID(shortReadMarker);
-			used[readID] = true;	
+			used[readID] = true;
 		}
-		
+
 		shortReadArray = getNodeReads(getTwinNode(node), graph);
 		shortReadCount = getNodeReadCount(getTwinNode(node), graph);
 		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
 			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
 			readID = getShortReadMarkerID(shortReadMarker);
-			used[readID] = true;	
+			used[readID] = true;
 		}
 	}
 
-	for (readID = 1; readID <= sequenceCount(graph); readID++) 
+	for (readID = 1; readID <= sequenceCount(graph); readID++)
 		if (used[readID])
 			res++;
 
-	free(used);	
+	free(used);
 
 	return res;
 }
@@ -1841,7 +1841,7 @@ void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *director
 {
 	char *logFilename =
 	    mallocOrExit(strlen(directory) + 100, char);
-	char *statsLine = 
+	char *statsLine =
 	    mallocOrExit(5000, char);
 	FILE *logFile;
 
@@ -1860,7 +1860,7 @@ void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *director
 	     (long) sequenceCount(graph));
 
 	velvetFprintf(logFile, "%s", statsLine);
-	velvetFprintf(stdout, "%s", statsLine);
+	//velvetFprintf(stdout, "%s", statsLine); //don't print to stdout when part of a library
 
 	fclose(logFile);
 	free(logFilename);
@@ -1888,16 +1888,16 @@ void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLe
 		node = getNodeInGraph(graph, nodeID);
 		if (node == NULL || getNodeLength(node) < minContigKmerLength)
 			continue;
-		
+
 		// Long reads
 		for(marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker)) {
 			readID = getPassageMarkerSequenceID(marker);
 			if (readID < 0)
 				readID = -readID;
-			used[readID] = true;	
-		}	
+			used[readID] = true;
+		}
 
-		// Short reads		
+		// Short reads
 		if (!readStartsAreActivated(graph))
 			continue;
 
@@ -1906,31 +1906,31 @@ void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLe
 		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
 			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
 			readID = getShortReadMarkerID(shortReadMarker);
-			used[readID] = true;	
+			used[readID] = true;
 		}
-		
+
 		shortReadArray = getNodeReads(getTwinNode(node), graph);
 		shortReadCount = getNodeReadCount(getTwinNode(node), graph);
 		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
 			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
 			readID = getShortReadMarkerID(shortReadMarker);
-			used[readID] = true;	
+			used[readID] = true;
 		}
 	}
 
-	for (readID = 1; readID <= sequenceCount(graph); readID++) 
+	for (readID = 1; readID <= sequenceCount(graph); readID++)
 		if (!used[readID])
 			exportTightString(outfile, getTightStringInArray(reads->tSequences, readID - 1), readID);
 
 	free(outFilename);
-	free(used);	
+	free(used);
 	fclose(outfile);
 }
 
 static IDnum getReferenceCount(ReadSet * reads) {
 	IDnum index;
 
-	for (index = 0; index < reads->readCount; index++) 
+	for (index = 0; index < reads->readCount; index++)
 		if (reads->categories[index] != REFERENCE)
 			break;
 
@@ -1979,7 +1979,7 @@ static ReferenceCoord * collectReferenceCoords(SequencesReader *seqReadInfo, IDn
 				start = longlongvar;
 				sscanf(strtok(NULL, ":-\r\n"), "%lli", &longlongvar);
 				finish = longlongvar;
-				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);  
+				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);
 				if (start <= finish) {
 					strcpy(refCoords[refIndex].name, name);
 					refCoords[refIndex].start = start;
@@ -1998,17 +1998,17 @@ static ReferenceCoord * collectReferenceCoords(SequencesReader *seqReadInfo, IDn
 				}
 
 				strcpy(name, line + 1);
-				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);  
+				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);
 				strcpy(refCoords[refIndex].name, name);
 				refCoords[refIndex].start = 1;
 				refCoords[refIndex].finish = -1;
 				refCoords[refIndex].positive_strand = true;
 			}
 			if (++refIndex == referenceCount)
-				break;	
+				break;
 		}
 	}
-	
+
 	fclose(file);
 	}
 	return refCoords;
@@ -2020,23 +2020,23 @@ typedef struct refMap_st {
 	IDnum refID;
 	IDnum refStart;
 	IDnum refFinish;
-} ATTRIBUTE_PACKED ReferenceMapping; 
+} ATTRIBUTE_PACKED ReferenceMapping;
 
 static int compareReferenceMappings(const void * A, const void * B) {
 	ReferenceMapping * refMapA = (ReferenceMapping *) A;
 	ReferenceMapping * refMapB = (ReferenceMapping *) B;
-	
+
 	if (refMapA->start < refMapB->start)
 		return -1;
 	else if (refMapA->start == refMapB->start)
 		return 0;
-	else 
+	else
 		return 1;
 }
 
 static void initializeReferenceMapping(ReferenceMapping * refMap, PassageMarkerI marker, Node * node) {
 	refMap->start = getStartOffset(marker);
-	refMap->finish = getNodeLength(node) - getFinishOffset(marker); 
+	refMap->finish = getNodeLength(node) - getFinishOffset(marker);
 	refMap->refID = getPassageMarkerSequenceID(marker);
 	refMap->refStart = getPassageMarkerStart(marker);
 	refMap->refFinish = getPassageMarkerFinish(marker);
@@ -2046,7 +2046,7 @@ static void velvetFprintfReferenceMapping(FILE * file, ReferenceMapping * mappin
 	ReferenceCoord * refCoord;
 	Coordinate start, finish;
 
-	if (mapping->refID > 0) 
+	if (mapping->refID > 0)
 		refCoord = &refCoords[mapping->refID - 1];
 	else
 		refCoord = &refCoords[-mapping->refID - 1];
@@ -2064,13 +2064,13 @@ static void velvetFprintfReferenceMapping(FILE * file, ReferenceMapping * mappin
 			start = refCoord->start + mapping->refStart + wordLength - 1;
 			finish = refCoord->start + mapping->refFinish + 1;
 		} else {
-			start = refCoord->finish - mapping->refStart; 
-			finish = refCoord->finish - mapping->refFinish + wordLength;  
+			start = refCoord->finish - mapping->refStart;
+			finish = refCoord->finish - mapping->refFinish + wordLength;
 		}
 	}
-		
+
 	velvetFprintf(file, "%lli\t%lli\t%s\t%lli\t%lli\n",
-		(long long) mapping->start + 1, (long long) mapping->finish + wordLength - 1, 
+		(long long) mapping->start + 1, (long long) mapping->finish + wordLength - 1,
 		refCoord->name, (long long) start, (long long) finish);
 }
 
@@ -2089,7 +2089,7 @@ static void exportLongNodeMapping(FILE * outfile, Node * node, ReadSet * reads,
 	velvetFprintf(outfile, ">contig_%li\n", (long) getNodeID(node));
 
 	// Create table
-	referenceMappings = callocOrExit(referenceCount, ReferenceMapping);	
+	referenceMappings = callocOrExit(referenceCount, ReferenceMapping);
 
 	// Initialize table
 	referenceCount = 0;
@@ -2115,9 +2115,9 @@ void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,
 	IDnum nodeIndex, refIndex;
 	Node *node;
 	ReferenceCoord * refCoords;
-	IDnum referenceCount = getReferenceCount(reads); 
+	IDnum referenceCount = getReferenceCount(reads);
 
-	if (referenceCount == 0)	
+	if (referenceCount == 0)
 		return;
 
 	refCoords = collectReferenceCoords(seqReadInfo, referenceCount);
@@ -2135,7 +2135,7 @@ void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,
 
 		if (node == NULL || getNodeLength(node) < minLength)
 			continue;
-		
+
 		exportLongNodeMapping(outfile, node, reads, refCoords, getWordLength(graph));
 	}
 

data/ext/src/src/run.c

@@ -39,7 +39,7 @@ static void printUsage()
 	printf("\thash_length\t: EITHER an odd integer (if even, it will be decremented) <= %i (if above, will be reduced)\n", MAXKMERLENGTH);
 	printf("\t\t\t: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= %i (if above, will be reduced)\n", MAXKMERLENGTH);
 	puts("\t\t\t\tand s is a step (even number). Velvet will then hash from k=m to k=M with a step of s");
-	puts("\tfilename\t: path to sequence file or - for standard input");	
+	puts("\tfilename\t: path to sequence file or - for standard input");
 	puts("");
 	puts("File format options:");
 	puts("\t-fasta\t-fastq\t-raw\t-fasta.gz\t-fastq.gz\t-raw.gz\t-sam\t-bam\t-fmtAuto");
@@ -52,7 +52,7 @@ static void printUsage()
 	puts("Read type options:");
 	puts("\t-short\t-shortPaired");
 #if CATEGORIES <= 5
-	Category cat; 
+	Category cat;
 	for (cat = 2; cat <= CATEGORIES; cat++)
 	    printf("\t-short%i\t-shortPaired%i\n", cat, cat);
 #else
@@ -93,7 +93,7 @@ static void printUsage()
 	puts("\t\t[Both files are picked up by graph, so please leave them there]");
 }
 
-int main(int argc, char **argv)
+int velveth(int argc, char **argv)
 {
 	ReadSet *allSequences = NULL;
 	SplayTable *splayTable;
@@ -161,18 +161,18 @@ int main(int argc, char **argv)
 		    ("Velvet can't handle k-mers as long as %i! We'll stick to %i if you don't mind.\n",
 		     hashLength, MAXKMERLENGTH);
 		hashLength = MAXKMERLENGTH;
-	} 
+	}
 	if (hashLength <= 0) {
 		velvetLog("Invalid hash length: %s\n", argv[2]);
 		printUsage();
 		return 0;
-	} 
+	}
 	if (hashLength % 2 == 0) {
 		velvetLog
 		    ("Velvet can't work with even length k-mers, such as %i. We'll use %i instead, if you don't mind.\n",
 		     hashLength, hashLength - 1);
 		hashLength--;
-	} 
+	}
 
 	if (multiple_kmers) {
 		if (hashLengthMax > MAXKMERLENGTH + 1) {
@@ -180,12 +180,12 @@ int main(int argc, char **argv)
 			    ("Velvet can't handle k-mers as long as %i! We'll stick to %i if you don't mind.\n",
 			     hashLengthMax, MAXKMERLENGTH + 1);
 			hashLengthMax = MAXKMERLENGTH + 1;
-		} 
+		}
 		if (hashLengthMax <= hashLength) {
 			velvetLog("hashLengthMin < hashLengthMax is required %s", argv[2]);
 			printUsage();
 			return 0;
-		} 
+		}
 
 		if (hashLengthStep <= 0) {
 			velvetLog("Non-positive hash length! Setting it to 2\n");
@@ -215,7 +215,7 @@ int main(int argc, char **argv)
 			sprintf(buf,"%s_%d",argv[1],h);
 			directory = mallocOrExit(strlen(buf) + 100, char);
 			strcpy(directory,buf);
-		} else 
+		} else
 			directory = argv[1];
 
 		filename = mallocOrExit(strlen(directory) + 100, char);

data/ext/src/src/run2.c

@@ -68,6 +68,8 @@ static void printUsage()
 	puts("\t-paired_exp_fraction <double>\t: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)");
 	puts("\t-shortMatePaired* <yes|no>\t: for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)");
 	puts("\t-conserveLong <yes|no>\t\t: preserve sequences with long reads in them (default no)");
+	puts("\t-clip_tips <yes|no>\t\t: do tip clipping on pre-graph (default yes)");
+	puts("\t-tour_bus <yes|no>\t\t: apply the tour bus algorithm (default yes)");
 	puts("");
 	puts("Output:");
 	puts("\tdirectory/contigs.fa\t\t: fasta file of contigs longer than twice hash length");
@@ -76,7 +78,7 @@ static void printUsage()
 	puts("\tdirectory/velvet_asm.afg\t: (if requested) AMOS compatible assembly file");
 }
 
-int main(int argc, char **argv)
+int velvetg(int argc, char **argv)
 {
 	ReadSet *sequences = NULL;
 	RoadMapArray *rdmaps;
@@ -86,7 +88,9 @@ int main(int argc, char **argv)
 	    *preGraphFilename, *seqFilename, *roadmapFilename,
 	    *lowCovContigsFilename, *highCovContigsFilename;
 	double coverageCutoff = -1;
-	double longCoverageCutoff = -1;
+  boolean doClipTips = true;
+  boolean doTourBus = true;
+  double longCoverageCutoff = -1;
 	double maxCoverageCutoff = -1;
 	double expectedCoverage = -1;
 	Coordinate minContigLength = -1;
@@ -164,7 +168,7 @@ int main(int argc, char **argv)
 		return 0;
 	}
 
-	// Memory allocation 
+	// Memory allocation
 	directory = argv[1];
 	graphFilename = mallocOrExit(strlen(directory) + 100, char);
 	connectedGraphFilename = mallocOrExit(strlen(directory) + 100, char);
@@ -181,9 +185,9 @@ int main(int argc, char **argv)
 		if (arg_index >= argc) {
 			velvetLog("Unusual number of arguments!\n");
 			printUsage();
-#ifdef DEBUG 
+#ifdef DEBUG
 			abort();
-#endif 
+#endif
 			exit(1);
 		}
 
@@ -210,9 +214,9 @@ int main(int argc, char **argv)
 			if (insertLength[0] < 0) {
 				velvetLog("Invalid insert length: %lli\n",
 				       (long long) insertLength[0]);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 		} else if (strcmp(arg, "-ins_length_sd") == 0) {
@@ -221,9 +225,9 @@ int main(int argc, char **argv)
 			if (std_dev[0] < 0) {
 				velvetLog("Invalid std deviation: %lli\n",
 				       (long long) std_dev[0]);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 		} else if (strcmp(arg, "-ins_length_long") == 0) {
@@ -238,9 +242,9 @@ int main(int argc, char **argv)
 			cat = (Category) short_var;
 			if (cat < 1 || cat > CATEGORIES) {
 				velvetLog("Unknown option: %s\n", arg);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 			sscanf(argv[arg_index], "%lli", &longlong_var);
@@ -248,9 +252,9 @@ int main(int argc, char **argv)
 			if (insertLength[cat - 1] < 0) {
 				velvetLog("Invalid insert length: %lli\n",
 				       (long long) insertLength[cat - 1]);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 		} else if (strncmp(arg, "-ins_length", 11) == 0) {
@@ -258,9 +262,9 @@ int main(int argc, char **argv)
 			cat = (Category) short_var;
 			if (cat < 1 || cat > CATEGORIES) {
 				velvetLog("Unknown option: %s\n", arg);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 			sscanf(argv[arg_index], "%lli", &longlong_var);
@@ -268,9 +272,9 @@ int main(int argc, char **argv)
 			if (std_dev[cat - 1] < 0) {
 				velvetLog("Invalid std deviation: %lli\n",
 				       (long long) std_dev[cat - 1]);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 		} else if (strcmp(arg, "-read_trkg") == 0) {
@@ -353,6 +357,12 @@ int main(int argc, char **argv)
 				exit(1);
 			}
 			shadows[cat - 1] = (strcmp(argv[arg_index], "yes") == 0);
+    } else if (strcmp(arg,"-clip_tips") == 0){
+      if (strcmp(argv[arg_index], "no") == 0)
+        doClipTips = false;
+    } else if (strcmp(arg,"-tour_bus") == 0){
+      if (strcmp(argv[arg_index], "no") == 0)
+        doTourBus = false;
 		} else if (strcmp(arg, "--help") == 0) {
 			printUsage();
 			return 0;
@@ -452,7 +462,8 @@ int main(int argc, char **argv)
 
 		sequenceLengths =
 		    getSequenceLengths(sequences, getWordLength(graph));
-		correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
+    if (doTourBus)
+        correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
 		exportGraph(graphFilename, graph, sequences->tSequences);
 	} else if ((file = fopen(preGraphFilename, "r")) != NULL) {
 		fclose(file);
@@ -468,7 +479,8 @@ int main(int argc, char **argv)
 				   roadmapFilename, readTracking, accelerationBits);
 		sequenceLengths =
 		    getSequenceLengths(sequences, getWordLength(graph));
-		correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
+    if (doTourBus)
+        correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
 		exportGraph(graphFilename, graph, sequences->tSequences);
 	} else if ((file = fopen(roadmapFilename, "r")) != NULL) {
 		fclose(file);
@@ -509,7 +521,7 @@ int main(int argc, char **argv)
 		}
 		preGraph = newPreGraph_pg(rdmaps, seqReadInfo);
 		concatenatePreGraph_pg(preGraph);
-		if (!conserveLong)
+		if (!conserveLong && doClipTips)
 		    clipTips_pg(preGraph);
 		exportPreGraph_pg(preGraphFilename, preGraph);
 		destroyPreGraph_pg(preGraph);
@@ -523,13 +535,14 @@ int main(int argc, char **argv)
 				   roadmapFilename, readTracking, accelerationBits);
 		sequenceLengths =
 		    getSequenceLengths(sequences, getWordLength(graph));
-		correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
+    if (doTourBus)
+        correctGraph(graph, sequenceLengths, sequences->categories, conserveLong);
 		exportGraph(graphFilename, graph, sequences->tSequences);
 	} else {
 		velvetLog("No Roadmap file to build upon! Please run velveth (see manual)\n");
-#ifdef DEBUG 
+#ifdef DEBUG
 		abort();
-#endif 
+#endif
 		exit(1);
 	}
 
@@ -553,11 +566,11 @@ int main(int argc, char **argv)
 			coverageCutoff = expectedCoverage / 2;
 			estimateCutoff = true;
 		}
-	} else { 
+	} else {
 		estimateCoverage = false;
-		if (coverageCutoff < 0 && estimateCutoff) 
+		if (coverageCutoff < 0 && estimateCutoff)
 			coverageCutoff = estimated_cov(graph, directory) / 2;
-		else 
+		else
 			estimateCutoff = false;
 	}
 
@@ -580,7 +593,7 @@ int main(int argc, char **argv)
 	if (minContigLength < 2 * getWordLength(graph))
 		minContigKmerLength = getWordLength(graph);
 	else
-		minContigKmerLength = minContigLength - getWordLength(graph) + 1;		
+		minContigKmerLength = minContigLength - getWordLength(graph) + 1;
 
 	dubious =
 	    removeLowCoverageNodesAndDenounceDubiousReads(graph,
@@ -599,7 +612,8 @@ int main(int argc, char **argv)
 							  lowCovContigsFilename);
 
 	removeHighCoverageNodes(graph, maxCoverageCutoff, exportFilteredNodes, minContigKmerLength, highCovContigsFilename);
-	clipTipsHard(graph, conserveLong);
+	if (doClipTips)
+		clipTipsHard(graph, conserveLong);
 
 	if (sequences->readCount > 0 && sequences->categories[0] == REFERENCE)
 		removeLowArcs(graph, coverageCutoff);
@@ -635,7 +649,7 @@ int main(int argc, char **argv)
 	strcpy(graphFilename, directory);
 	strcat(graphFilename, "/contigs.fa");
 	sequenceLengths = getSequenceLengths(sequences, getWordLength(graph));
-	exportLongNodeSequences(graphFilename, graph, minContigKmerLength, sequences, sequenceLengths, coverageMask); 
+	exportLongNodeSequences(graphFilename, graph, minContigKmerLength, sequences, sequenceLengths, coverageMask);
 
 	if (exportAlignments) {
 		strcpy(graphFilename, directory);
@@ -663,9 +677,9 @@ int main(int argc, char **argv)
 	if (unusedReads)
 		exportUnusedReads(graph, sequences, minContigKmerLength, directory);
 
-	if (estimateCoverage) 
+	if (estimateCoverage)
 		velvetLog("Estimated Coverage = %f\n", expectedCoverage);
-	if (estimateCutoff) 
+	if (estimateCutoff)
 		velvetLog("Estimated Coverage cutoff = %f\n", coverageCutoff);
 
 	logFinalStats(graph, minContigKmerLength, directory);
@@ -673,25 +687,25 @@ int main(int argc, char **argv)
 	if (clean > 0) {
 		strcpy(graphFilename, directory);
 		strcat(graphFilename, "/Roadmaps");
-		remove(graphFilename);	
+		remove(graphFilename);
 
 		strcpy(graphFilename, directory);
 		strcat(graphFilename, "/LastGraph");
-		remove(graphFilename);	
-	} 
+		remove(graphFilename);
+	}
 
 	if (clean > 1) {
 		strcpy(graphFilename, directory);
 		strcat(graphFilename, "/Sequences");
-		remove(graphFilename);	
+		remove(graphFilename);
 
 		strcpy(graphFilename, directory);
 		strcat(graphFilename, "/Graph2");
-		remove(graphFilename);	
+		remove(graphFilename);
 
 		strcpy(graphFilename, directory);
 		strcat(graphFilename, "/Graph");
-		remove(graphFilename);	
+		remove(graphFilename);
 	}
 
 	free(sequenceLengths);

data/ext/src/src/utility.c

@@ -1,5 +1,5 @@
 /*
-Copyright 2009 John Marshall (jm18@sanger.ac.uk) 
+Copyright 2009 John Marshall (jm18@sanger.ac.uk)
 
     This file is part of Velvet.
 
@@ -89,14 +89,15 @@ void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)
        fprintf(stderr, "\n");
        va_end(args);
 
-#ifdef DEBUG 
+#ifdef DEBUG
 	abort();
-#endif 
+#endif
        exit(exitStatus);
 }
 
 void velvetLog(const char *format, ...)
 {
+  /*     Don't print anything as it interferes with code bound through bioruby-velvet_underground
   static boolean timeIsSet = false;
   static struct timeval tvStart;
   struct timeval tvNow;
@@ -117,14 +118,14 @@ void velvetLog(const char *format, ...)
   vprintf(format, args);
   va_end(args);
 
-#ifdef DEBUG 
+#ifdef DEBUG
   fflush(stdout);
-#endif
+#endif*/
 }
 
-void velvetFprintf(FILE * file, const char * format, ...) 
+void velvetFprintf(FILE * file, const char * format, ...)
 {
-	va_list args;
+  va_list args;
 
 	va_start(args, format);
 	if (vfprintf(file, format, args) < 0) {
@@ -132,9 +133,9 @@ void velvetFprintf(FILE * file, const char * format, ...)
 		       fprintf(stderr, "%s: ", programName);
 		fprintf(stderr, "Could not write into file\n");
 		va_end(args);
-#ifdef DEBUG 
+#ifdef DEBUG
 		abort();
-#endif 
+#endif
 		exit(EXIT_FAILURE);
 	}
 	va_end(args);

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet_underground
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Ben Woodcroft