bio-velvet_underground 0.0.1 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitmodules

@@ -1,3 +1,4 @@
 [submodule "ext/src"]
 	path = ext/src
+	branch = underground
 	url = https://github.com/wwood/velvet

data/.rspec

@@ -0,0 +1 @@
+--color

data/Gemfile

@@ -4,6 +4,7 @@ source "http://rubygems.org"
 #   gem "activesupport", ">= 2.3.5"
 
 gem 'ffi', '~> 1.9'
+gem 'bio-logger', '~> 1.0'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/README.md

@@ -2,34 +2,78 @@
 
 [![Build Status](https://secure.travis-ci.org/wwood/bioruby-velvet_underground.png)](http://travis-ci.org/wwood/bioruby-velvet_underground)
 
-This biogem is aimed at providing Ruby bindings to the velvet assembler's source code.
-
-Note: this software is under active development!
+This biogem is aimed at providing Ruby bindings to the velvet assembler's source code. See also [bio-velvet](https://github.com/wwood/bioruby-velvet) for Ruby code that does not bind the velvet C.
 
 ## Installation
 
 ```sh
 gem install bio-velvet_underground
 ```
+This can take a few minutes as several versions of velvet with different kmer sizes are compiled.
 
 ## Usage
 
-The only thing implemented at this stage is access to the binary sequence file created when velveth is run with the `-create_binary` flag.
+The code is intended to cater for a few specific purposes.
 
+### Running velvet
+Running velvet returns a `Result` object, which is effectively a pointer to a velvet result directory
 ```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
+
+# A pre-defined velvet result directory:
+result = Bio::Velvet::Runner.new.velvet(29,"-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).
+Several libraries are pre-compiled at gem install-time, and then bound at runtime. `velveth` and `velvetg`
+steps can be run separetely if required.
+
+### Working with the binary sequence file
+The binary sequence file created when velveth is run with the `-create_binary` flag.
+
+```ruby
 seqs = Bio::Velvet::Underground::BinarySequenceStore.new '/path/to/velvet/directory/CnyUnifiedSeq'
-seqs[1] #=> 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGA'
 seqs.length #=> 77 (there is 77 sequences in the CnyUnifiedSeq)
+seqs[1] #=> 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGA'
+seqs[0] #=> nil (indices map directly to the indices in other velvet files)
+```
 
+### Working with LastGraph file
+```ruby
+path = 'spec/data/3/Assem/LastGraph'
+graph = Bio::Velvet::Underground::Graph.parse_from_file path #=> Bio::Velvet::Underground::Graph object
+
+graph.hash_length #=> 31 (kmer length)
+graph.node_count #=> 4
+
+graph.nodes[1] #=> Bio::Velvet::Underground::Graph::Node object
+graph.nodes[2].ends_of_kmers_of_node #=> 'GTTTAAAAGAAGGAGATTACTTTATAAAA'
+graph.nodes[2].coverages #=> [58,0] (coverages from different categories)
+
+graph.nodes[1].short_reads #=> Array of Bio::Velvet::Underground::Graph::NodedRead objects
+graph.nodes[1].short_reads[0].direction #=> true (i.e. forward w.r.t the node)
+graph.nodes[1].short_reads[2].read_id #=> 4
 ```
+There are more to these objects - see the documention.
+
+
+Patches to these and other parts of velvet welcome.
+
+## Development practice
+
+The velvet C code 'underground' here is for the most part vanilla velvet code as you might expect.
+However some changes were necessary to allow binding from this biogem. For instance the library
+does not write to `$stdout` as this interferes with Ruby's writes to `$stdout`.
 
-Patches to other parts of velvet welcome.
+There are also some extra options for controlling velvet's behaviour, geared towards taking 
+some of the guesswork out of the assembly process at the expense of a less resolved `LastGraph`.
+These are currently non-standard modifications - get in touch with @wwood if you are interested. 
+Not invoking these options should leave 'normal' velvet behaviour intact.
 
-The API doc is online. For more code examples see the test files in
-the source tree.
-        
 ## Project home page
 
 Information on the source tree, documentation, examples, issues and

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

data/ext/mkrf_conf.rb

@@ -22,15 +22,33 @@ require 'rake/clean'
 path = File.expand_path(File.dirname(__FILE__))
 path_external = File.join(File.dirname(__FILE__), "../lib/bio-velvet_underground/external")
 
+# Require constants - code shared between before and after installation
+require File.join(File.dirname(__FILE__), "../lib/bio-velvet_underground/constants")
+
 task :compile do
   cd(File.join(File.dirname(__FILE__),'src')) do
-    sh "patch -p1 < ../bioruby.patch"
     case Config::CONFIG['host_os']
       when /linux/
-      sh "make shared"
-      cp("obj/shared/libvelvet.so.1.0",path_external)
+
+        # Create library with default install params
+        $stdout.puts "Making velvet shared library with default parameters"
+        sh "make shared"
+        shared_location = 'obj/shared'
+        cp(File.join(shared_location,"libvelvet.so.1.0"), path_external)
+        $stdout.puts "Finished installing default library version"
+        # Create libraries with larger non-default kmer sizes
+        Bio::Velvet::Underground.max_kmers.each do |max_kmer|
+          next if max_kmer == Bio::Velvet::Underground::DEFAULT_MAXKMERLENGTH
+
+          $stdout.puts "Making velvet shared library with kmer "+max_kmer.to_s
+          library_name = File.basename Bio::Velvet::Underground.library_location_of(max_kmer)
+          sh "make clean; make MAXKMERLENGTH="+max_kmer.to_s+" shared"
+          cp(File.join(shared_location,"libvelvet.so.1.0"),
+          File.join(path_external,File.basename(library_name)))
+        end
+
       when /darwin/
-      raise NotImplementedError, "possibly will work, but bio-velvet_underground is not tested on OSX"
+        raise NotImplementedError, "possibly will work, but bio-velvet_underground is not tested on OSX"
       when /mswin|mingw/ then raise NotImplementedError, "bio-velvet_underground library is not available for Windows platform"
     end #case
   end #cd

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:
@@ -2094,9 +2094,11 @@ static void cleanUpRedundancy()
 		if (isTerminal(slowMarker))
 			slowLength = finalLength;
 		else {
-			slowLength =
-			    slowToFastMapping[getPassageMarkerFinish
-					      (slowMarker) - 1];
+			if(getPassageMarkerFinish(slowMarker) != 0)
+				slowLength = slowToFastMapping[getPassageMarkerFinish(slowMarker) - 1];
+			else
+				slowLength = slowToFastMapping[0];
+
 			if (slowLength < slowConstraint)
 				slowLength = slowConstraint;
 		}
@@ -2165,7 +2167,7 @@ static void cleanUpRedundancy()
 
 	//velvetLog("Concatenation\n");
 
-	// Freeing up memory  
+	// Freeing up memory
 	if (slowMarker != NULL_IDX)
 		concatenatePathNodes(slowPath);
 	else
@@ -2458,7 +2460,7 @@ void clipTipsHard(Graph * graph, boolean conserveLong)
 
 			if (current == NULL)
 				continue;
-	
+
 			if (conserveLong && getMarker(current))
 				continue;
 
@@ -2558,7 +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();
@@ -2605,9 +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;
@@ -2619,9 +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;
@@ -2633,9 +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/graph.c

@@ -906,7 +906,7 @@ void appendDescriptors(Node * destination, Node * source)
 	twinDestination->length = newLength;
 }
 
-static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength) 
+static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength)
 {
 	Coordinate index;
 	Nucleotide nucleotide;
@@ -917,7 +917,7 @@ static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Des
 	}
 }
 
-static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength) 
+static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength)
 {
 	Coordinate shift = totalLength - destinationLength - sourceLength;
 	Coordinate index;
@@ -2052,7 +2052,7 @@ Graph *importGraph(char *filename)
 	short short_var;
 	char c;
 
-	if (file == NULL) 
+	if (file == NULL)
 		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
 
 	velvetLog("Reading graph file %s\n", filename);
@@ -2204,9 +2204,9 @@ Graph *importGraph(char *filename)
 				velvetLog
 				    ("ERROR: reading in graph - only %d items read for line '%s'",
 				     sCount, line);
-#ifdef DEBUG 
+#ifdef DEBUG
 				abort();
-#endif 
+#endif
 				exit(1);
 			}
 			newMarker =
@@ -2404,7 +2404,7 @@ Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand)
 #endif
 				}
 			}
-			
+
 			index++;
 		}
 
@@ -2506,7 +2506,7 @@ Graph *readConnectedGraphFile(char *connectedGraphFilename, boolean * double_str
 		twin = node->twinNode;
 		twin->length = node->length;
 		twin->descriptor =
-			callocOrExit(arrayLength, Descriptor);   
+			callocOrExit(arrayLength, Descriptor);
 
 		index = 0;
 		while ((c = getc(file)) != '\n') {
@@ -3145,9 +3145,13 @@ ShortReadMarker *extractFrontOfNodeReads(Node * node,
 	}
 
 	free(sourceArray);
-	graph->nodeReads[sourceID] = newArray;
 	graph->nodeReadCounts[sourceID] = newLength;
 
+	if(newLength > 0)
+		graph->nodeReads[sourceID] = newArray;
+	else
+		graph->nodeReads[sourceID] = NULL;
+
 	*length = mergeLength;
 	return mergeArray;
 }
@@ -3275,9 +3279,13 @@ ShortReadMarker *extractBackOfNodeReads(Node * node, Coordinate breakpoint,
 	}
 
 	free(sourceArray);
-	graph->nodeReads[sourceID] = newArray;
 	graph->nodeReadCounts[sourceID] = newLength;
 
+	if(newLength > 0)
+		graph->nodeReads[sourceID] = newArray;
+	else
+		graph->nodeReads[sourceID] = NULL;
+
 	*length = mergeLength;
 	return mergeArray;
 }
@@ -3321,8 +3329,13 @@ void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,
 			sourceIndex++;
 		}
 
-		graph->nodeReads[targetID] = mergeArray;
 		graph->nodeReadCounts[targetID] = sourceLength;
+
+		if(sourceLength > 0)
+		    graph->nodeReads[targetID] = mergeArray;
+		else
+		    graph->nodeReads[targetID] = NULL;
+
 		return;
 	}
 
@@ -3402,8 +3415,12 @@ void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,
 	}
 
 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;
+
+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
 }
 
 static inline Coordinate min(Coordinate A, Coordinate B)
@@ -3437,8 +3454,13 @@ void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,
 
 	if (targetLength == 0) {
 		free(targetArray);
-		graph->nodeReads[targetID] = sourceArray;
 		graph->nodeReadCounts[targetID] = sourceLength;
+
+		if(sourceLength > 0)
+			graph->nodeReads[targetID] = sourceArray;
+		else
+			graph->nodeReads[targetID] = NULL;
+
 		return;
 	}
 
@@ -3548,9 +3570,13 @@ void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,
 	}
 
 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;
 
+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
+
 	free(sourceArray);
 }
 
@@ -3693,12 +3719,20 @@ void foldSymmetricalNodeReads(Node * node, Graph * graph)
 	}
 
 	free(targetArray);
-	graph->nodeReads[targetID] = mergeArray;
 	graph->nodeReadCounts[targetID] = mergeLength;
 
+	if(mergeLength > 0)
+		graph->nodeReads[targetID] = mergeArray;
+	else
+		graph->nodeReads[targetID] = NULL;
+
 	free(sourceArray);
-	graph->nodeReads[sourceID] = mergeArray2;
 	graph->nodeReadCounts[sourceID] = mergeLength;
+
+	if(mergeLength > 0)
+		graph->nodeReads[sourceID] = mergeArray2;
+	else
+		graph->nodeReads[sourceID] = NULL;
 }
 
 void shareReadStarts(Node * target, Node * source, Graph * graph)
@@ -3973,7 +4007,7 @@ void reallocateNodeDescriptor(Node * node, Coordinate length) {
 		nucleotide = getNucleotideInDescriptor(twin->descriptor, index);
 		writeNucleotideInDescriptor(nucleotide, array, index + shift);
 	}
-	
+
 	free(twin->descriptor);
 	twin->descriptor = array;
 }