bio-velvet_underground 0.0.1 → 0.1.0

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);