bio-velvet_underground 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: bc8d0a17768ec2f94fd304c98a58505229b2a955
+  metadata.gz: 696cf2a0e11ae0c6848fe4d717e1add4e1452370
+  data.tar.gz: 3b88bb295352c038eddeb118835e88596b66641b
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+  data.tar.gz: a0331bd42caecc5adbb2fde466e2c8ea6de71db07c621f844a8ccc9456e78ef13ea1ce41073052bd574e32655676c057d3854a44c9875bedad1314c322746345

data/README.md

@@ -20,12 +20,10 @@ Running velvet returns a `Result` object, which is effectively a pointer to a ve
 ```ruby
 require 'bio-velvet_underground'
 
-#kmer 29, '-short my.fasta' the argument to velveth, no special arguments given to velvetg.
-result = Bio::Velvet::Runner.new.velvet(29,"-short my.fasta",'')
-result.result_directory #=> path to temporary directory, containing velvet generated files e.g. contigs.fna
-
+# Run assembly with kmer 29, '-short my.fasta' the arguments to velveth (not including kmer and directory),
+# no special arguments given to velvetg.
 # A pre-defined velvet result directory:
-result = Bio::Velvet::Runner.new.velvet(29,"-short my.fasta",'',:output_assembly_path => '/path/to/result')
+result = Bio::Velvet::Runner.new.velvet(29, %w(-short my.fasta),[],:output_assembly_path => '/path/to/result')
 result.result_directory #=> '/path/to/result'
 ```
 With the magic of Ruby-FFI, the library with the smallest kmer size >= 29 is chosen (in this case 31).

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/ext/src/Makefile

@@ -3,8 +3,8 @@ CFLAGS = -Wall
 DEBUG = -g
 LIBS = -lm
 OPT = -O3
-MAXKMERLENGTH=31
-CATEGORIES=2
+MAXKMERLENGTH?=31
+CATEGORIES?=2
 DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
 PDFLATEX_VERSION := $(shell pdflatex --version 2> /dev/null)
 
@@ -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
@@ -39,24 +39,23 @@ 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 : zlib obj velveth velvetg
+default : cleanobj zlib obj velveth velvetg doc
 
 clean : clean-zlib
-	-rm obj/*.o obj/dbg/*.o obj/shared/*.o obj/shared/velvet.so.0.0.1 ./velvet*
+	-rm obj/*.o obj/dbg/*.o ./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 obj/shared/*.o
+cleanobj: 
+	-rm obj/*.o obj/dbg/*.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 :
@@ -68,14 +67,14 @@ 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)
@@ -93,25 +92,25 @@ colordebug : cleanobj obj/dbg_de
 objdir:
 	mkdir -p obj
 
-obj: zlib objdir $(OBJ)
+obj: zlib cleanobj 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
 
@@ -124,15 +123,3 @@ 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); //don't print to stdout when part of a library
+	velvetFprintf(stdout, "%s", statsLine);
 
 	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));
 	}