Version 1.2.10 of Velvet: diff between the tarball downloaded from EBI and the version on GitHub

v1.2.10.patch

diff --git a/Makefile b/Makefile
index 3e47adc..a4b46e2 100644
--- a/Makefile
+++ b/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)
 
diff --git a/src/correctedGraph.c b/src/correctedGraph.c
index bdbf016..6e295f0 100644
--- a/src/correctedGraph.c
+++ b/src/correctedGraph.c
@@ -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;
 		}
diff --git a/src/graph.c b/src/graph.c
index 826979c..7dd857b 100644
--- a/src/graph.c
+++ b/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;
 }
diff --git a/src/scaffold.h b/src/scaffold.h
index bd61e28..f14e1c8 100644
--- a/src/scaffold.h
+++ b/src/scaffold.h
@@ -18,7 +18,7 @@ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
     Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
 */
-#ifndef _SSCAFFOLD_H_
+#ifndef _SCAFFOLD_H_
 #define _SCAFFOLD_H_
 
 typedef struct connection_st Connection;