!_TAG_FILE_FORMAT	2	/extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED	1	/0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR	Darren Hiebert	/dhiebert@users.sourceforge.net/
!_TAG_PROGRAM_NAME	Exuberant Ctags	//
!_TAG_PROGRAM_URL	http://ctags.sourceforge.net	/official site/
!_TAG_PROGRAM_VERSION	5.6	//
ADENINE	graph.c	33;"	d	file:
ADENINE	graphReConstruction.c	42;"	d	file:
ADENINE	preGraph.c	38;"	d	file:
ADENINE	preGraphConstruction.c	35;"	d	file:
ATTRIBUTE_PACKED	correctedGraph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:tkt_st
ATTRIBUTE_PACKED	graph.c	/^}  ATTRIBUTE_PACKED;	\/\/ 352 Total$/;"	v	typeref:struct:arc_st
ATTRIBUTE_PACKED	graph.c	/^} ATTRIBUTE_PACKED;	\/\/ 418 Total$/;"	v	typeref:struct:node_st
ATTRIBUTE_PACKED	graph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:gapMarker_st
ATTRIBUTE_PACKED	graph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:shortReadMarker_st
ATTRIBUTE_PACKED	graphReConstruction.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:nodeMask_st
ATTRIBUTE_PACKED	graphReConstruction.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:referenceMapping_st
ATTRIBUTE_PACKED	graphReConstruction.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:smallNodeList_st
ATTRIBUTE_PACKED	graphStats.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:referenceCoord_st
ATTRIBUTE_PACKED	kmerOccurenceTable.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:kmerOccurence_st
ATTRIBUTE_PACKED	passageMarker.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:passage_st
ATTRIBUTE_PACKED	preGraph.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:preNode_st
ATTRIBUTE_PACKED	preGraph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:preArc_st
ATTRIBUTE_PACKED	preGraph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:preMarker_st
ATTRIBUTE_PACKED	preGraphConstruction.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:insertionMarker_st
ATTRIBUTE_PACKED	readCoherentGraph.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:rb_connection_st
ATTRIBUTE_PACKED	readSet.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:referenceCoordinateTable_st
ATTRIBUTE_PACKED	readSet.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:referenceCoordinate_st
ATTRIBUTE_PACKED	roadMap.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:annotation_st
ATTRIBUTE_PACKED	roadMap.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:roadmap_st
ATTRIBUTE_PACKED	roadMap.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:union:positionPtr
ATTRIBUTE_PACKED	scaffold.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:connection_st
ATTRIBUTE_PACKED	scaffold.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:readOccurence_st
ATTRIBUTE_PACKED	shortReadPairs.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:miniConnection_st
ATTRIBUTE_PACKED	splay.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:splayNode_st
ATTRIBUTE_PACKED	tightString.c	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:tString_st
Adenine	tightString.c	/^static const Nucleotide Adenine = 0;$/;"	v	file:
AllocArrayFreeElement_st	allocArray.c	/^struct AllocArrayFreeElement_st {$/;"	s	file:
Arc	run.c	26;"	d	file:
BACKTRACK_CUTOFF	shortReadPairs.c	38;"	d	file:
BAM	readSet.c	1559;"	d	file:
BLOCKSIZE	dfib.c	57;"	d	file:
BLOCKSIZE	fib.c	57;"	d	file:
BLOCKSIZE	graph.c	91;"	d	file:
BLOCKSIZE	graphReConstruction.c	139;"	d	file:
BLOCKSIZE	readCoherentGraph.c	61;"	d	file:
BLOCKS_ALLOC_SIZE	allocArray.c	31;"	d	file:
BLOCKS_ALLOC_SIZE	allocArray.c	34;"	d	file:
BLOCK_SIZE	scaffold.c	40;"	d	file:
BLOCK_SIZE	shortReadPairs.c	36;"	d	file:
BUFFER_APPEND	splayTable.c	261;"	d	file:
CHARS	kmer.c	39;"	d	file:
CHUNKSIZE	splay.c	33;"	d	file:
CRC_HASH_BUCKETS	crc.c	26;"	d	file:
CRC_HASH_MASK	crc.c	23;"	d	file:
CYTOSINE	graph.c	34;"	d	file:
CYTOSINE	graphReConstruction.c	43;"	d	file:
CYTOSINE	preGraph.c	39;"	d	file:
CYTOSINE	preGraphConstruction.c	36;"	d	file:
Chunk	recycleBin.c	/^} Chunk;$/;"	t	typeref:struct:chunk_st	file:
Codon	tightString.c	/^typedef unsigned char Codon;$/;"	t	file:
Cytosine	tightString.c	/^static const Nucleotide Cytosine = 1;$/;"	v	file:
DECLARE_FAST_ACCESSORS	preGraph.c	/^DECLARE_FAST_ACCESSORS (PREARC, PreArc, preArcMemory)$/;"	f
DOTNode	graph.c	/^void DOTNode(Node * node, FILE * outfile)$/;"	f
ELAND	readSet.c	1554;"	d	file:
FASTA	readSet.c	1552;"	d	file:
FASTA_GZ	readSet.c	1555;"	d	file:
FASTQ	readSet.c	1551;"	d	file:
FASTQ_GZ	readSet.c	1556;"	d	file:
FAST_TO_SLOW	correctedGraph.c	2096;"	d	file:
FILTER0	tightString.c	/^static const Codon FILTER0 = ~((Codon) 3);$/;"	v	file:
FILTER1	tightString.c	/^static const Codon FILTER1 = ~(((Codon) 3) << 2);$/;"	v	file:
FILTER2	tightString.c	/^static const Codon FILTER2 = ~(((Codon) 3) << 4);$/;"	v	file:
FILTER3	tightString.c	/^static const Codon FILTER3 = (Codon) ~ ((Codon) 3 << 6);$/;"	v	file:
Fmatrix	correctedGraph.c	/^static double **Fmatrix;$/;"	v	file:
Fmatrix	locallyCorrectedGraph.c	/^static double **Fmatrix;$/;"	v	file:
GAPBLOCKSIZE	graph.c	92;"	d	file:
GERALD	readSet.c	1553;"	d	file:
GUANINE	graph.c	35;"	d	file:
GUANINE	graphReConstruction.c	44;"	d	file:
GUANINE	preGraph.c	40;"	d	file:
GUANINE	preGraphConstruction.c	37;"	d	file:
Guanine	tightString.c	/^static const Nucleotide Guanine = 2;$/;"	v	file:
ID	graph.c	/^	IDnum ID;		\/\/ 32$/;"	m	struct:node_st	file:
INDEL	correctedGraph.c	/^static const Time INDEL = 0;$/;"	v	file:
INDEL	locallyCorrectedGraph.c	/^static const Time INDEL = 0;$/;"	v	file:
INTS	kmer.c	40;"	d	file:
INT_BITS	dfib.c	81;"	d	file:
INT_BITS	fib.c	77;"	d	file:
LISTBLOCKSIZE	passageMarker.c	/^static const int LISTBLOCKSIZE = 10000;$/;"	v	file:
LN2	readCoherentGraph.c	34;"	d	file:
LN2	scaffold.c	41;"	d	file:
LN2	shortReadPairs.c	37;"	d	file:
LONGLONGS	kmer.c	42;"	d	file:
LONGS	kmer.c	41;"	d	file:
LONG_NODE_CUTOFF	readCoherentGraph.c	33;"	d	file:
MAQ_GZ	readSet.c	1557;"	d	file:
MAXDIVERGENCE	correctedGraph.c	/^static double MAXDIVERGENCE = 0.2;$/;"	v	file:
MAXDIVERGENCE	locallyCorrectedGraph.c	/^static double MAXDIVERGENCE = 0.2;$/;"	v	file:
MAXGAPS	correctedGraph.c	/^static int MAXGAPS = 3;$/;"	v	file:
MAXGAPS	locallyCorrectedGraph.c	/^static int MAXGAPS = 3;$/;"	v	file:
MAXNODELENGTH	correctedGraph.c	/^static int MAXNODELENGTH = 200;$/;"	v	file:
MAXNODELENGTH	locallyCorrectedGraph.c	/^static int MAXNODELENGTH = 200;$/;"	v	file:
MAXREADLENGTH	correctedGraph.c	/^static int MAXREADLENGTH = 100;$/;"	v	file:
MAXREADLENGTH	locallyCorrectedGraph.c	/^static int MAXREADLENGTH = 100;$/;"	v	file:
MAX_READ_COUNT	readCoherentGraph.c	36;"	d	file:
MAX_READ_LENGTH	readCoherentGraph.c	37;"	d	file:
MULTIPLICITY_CUTOFF	readCoherentGraph.c	/^static int MULTIPLICITY_CUTOFF = 2;$/;"	v	file:
MiniConnection	shortReadPairs.c	/^typedef struct miniConnection_st MiniConnection;$/;"	t	typeref:struct:miniConnection_st	file:
NB_PAGES_ALLOC	allocArray.c	30;"	d	file:
NB_PAGES_ALLOC	allocArray.c	33;"	d	file:
NULL	roadMap.c	34;"	d	file:
NodeMask	graphReConstruction.c	/^typedef struct nodeMask_st NodeMask;$/;"	t	typeref:struct:nodeMask_st	file:
PROBABILITY_CUTOFF	readCoherentGraph.c	35;"	d	file:
PassageMarker	passageMarker.c	/^typedef struct passage_st PassageMarker;$/;"	t	typeref:struct:passage_st	file:
PreArc	preGraph.c	/^typedef struct preArc_st PreArc;$/;"	t	typeref:struct:preArc_st	file:
RAW	readSet.c	1560;"	d	file:
RAW_GZ	readSet.c	1561;"	d	file:
RBConnection	readCoherentGraph.c	/^typedef struct rb_connection_st RBConnection;$/;"	t	typeref:struct:rb_connection_st	file:
ReadOccurence	scaffold.c	/^typedef struct readOccurence_st ReadOccurence;$/;"	t	typeref:struct:readOccurence_st	file:
RecycleBin_Node	recycleBin.c	/^typedef struct RecycleBin_Node {$/;"	s	file:
RecycleBin_Node	recycleBin.c	/^} RecycleBin_Node;$/;"	t	typeref:struct:RecycleBin_Node	file:
RecycleBin_memory_usage	recycleBin.c	/^size_t RecycleBin_memory_usage(RecycleBin * recycle_bin)$/;"	f
ReferenceCoord	graphStats.c	/^typedef struct referenceCoord_st ReferenceCoord;$/;"	t	typeref:struct:referenceCoord_st	file:
ReferenceCoordinate	readSet.c	/^typedef struct referenceCoordinate_st ReferenceCoordinate;$/;"	t	typeref:struct:referenceCoordinate_st	file:
ReferenceCoordinateTable	readSet.c	/^typedef struct referenceCoordinateTable_st ReferenceCoordinateTable;$/;"	t	typeref:struct:referenceCoordinateTable_st	file:
ReferenceMapping	graphReConstruction.c	/^typedef struct referenceMapping_st ReferenceMapping;$/;"	t	typeref:struct:referenceMapping_st	file:
ReferenceMapping	graphStats.c	/^} ATTRIBUTE_PACKED ReferenceMapping; $/;"	t	typeref:struct:refMap_st	file:
SAM	readSet.c	1558;"	d	file:
SELF_LOOP_CUTOFF	locallyCorrectedGraph.c	/^static int SELF_LOOP_CUTOFF;$/;"	v	file:
SET_BINARY_MODE	readSet.c	41;"	d	file:
SET_BINARY_MODE	readSet.c	43;"	d	file:
SIM	correctedGraph.c	/^static const Time SIM[4][4] = {$/;"	v	file:
SIM	locallyCorrectedGraph.c	/^static const Time SIM[4][4] = {$/;"	v	file:
SLOW_TO_FAST	correctedGraph.c	2095;"	d	file:
SingleRotateWithLeft	splay.c	/^static SplayNode *SingleRotateWithLeft(SplayNode * K2)$/;"	f	file:
SingleRotateWithRight	splay.c	/^static SplayNode *SingleRotateWithRight(SplayNode * K1)$/;"	f	file:
SmallNodeList	graphReConstruction.c	/^typedef struct smallNodeList_st SmallNodeList;$/;"	t	typeref:struct:smallNodeList_st	file:
Splay	splay.c	/^static SplayTree *Splay(Kmer * kmer, SplayTree * T)$/;"	f	file:
SplayNode	splay.c	/^typedef struct splayNode_st SplayNode;$/;"	t	typeref:struct:splayNode_st	file:
SplayTree	splay.c	/^typedef struct splayNode_st SplayTree;$/;"	t	typeref:struct:splayNode_st	file:
THYMINE	graph.c	36;"	d	file:
THYMINE	graphReConstruction.c	45;"	d	file:
THYMINE	preGraph.c	41;"	d	file:
THYMINE	preGraphConstruction.c	38;"	d	file:
TICKET_BLOCK_SIZE	correctedGraph.c	36;"	d	file:
Thymine	tightString.c	/^static const Nucleotide Thymine = 3;$/;"	v	file:
Ticket	correctedGraph.c	/^typedef struct tkt_st Ticket;$/;"	t	typeref:struct:tkt_st	file:
UNDEFINED	kmer.c	38;"	d	file:
UNRELIABLE_CONNECTION_CUTOFF	scaffold.c	/^static IDnum UNRELIABLE_CONNECTION_CUTOFF = 5;$/;"	v	file:
WORDLENGTH	correctedGraph.c	/^static int WORDLENGTH;$/;"	v	file:
WORDLENGTH	locallyCorrectedGraph.c	/^static int WORDLENGTH;$/;"	v	file:
WORDLENGTH	splayTable.c	/^	int WORDLENGTH;$/;"	m	struct:splayTable_st	file:
abs_ID	shortReadPairs.c	/^static IDnum abs_ID(IDnum val)$/;"	f	file:
abs_bool	shortReadPairs.c	/^static boolean abs_bool(boolean val)$/;"	f	file:
absorbExtension	shortReadPairs.c	/^static void absorbExtension(Node * node, Node * extension)$/;"	f	file:
absorbExtensionInScaffold	shortReadPairs.c	/^static void absorbExtensionInScaffold(Node * node, Node * source)$/;"	f	file:
accelerationBits	kmerOccurenceTable.c	/^	short int accelerationBits;$/;"	m	struct:kmerOccurenceTable_st	file:
accelerationShift	kmerOccurenceTable.c	/^	short int accelerationShift;$/;"	m	struct:kmerOccurenceTable_st	file:
accelerationTable	kmerOccurenceTable.c	/^	IDnum *accelerationTable;$/;"	m	struct:kmerOccurenceTable_st	file:
activateArcLookupTable	graph.c	/^void activateArcLookupTable(Graph * graph)$/;"	f
activateGapMarkers	graph.c	/^void activateGapMarkers(Graph * graph)$/;"	f
activateReadStarts	graph.c	/^void activateReadStarts(Graph * graph)$/;"	f
activeNode	correctedGraph.c	/^static Node *activeNode;$/;"	v	file:
addBufferToDescriptor	graph.c	/^static void addBufferToDescriptor(Node * node, Coordinate length)$/;"	f	file:
addEmptyNodeToGraph	graph.c	/^Node *addEmptyNodeToGraph(Graph * graph, IDnum ID)$/;"	f
addNodeToGraph	graph.c	/^void addNodeToGraph(Graph * graph, Node * node)$/;"	f
addPassageMarker	passageMarker.c	/^PassageMarkerI addPassageMarker(IDnum sequenceID, Coordinate start,$/;"	f
addPreArcToPreNode_pg	preGraph.c	/^static void addPreArcToPreNode_pg(PreArcI preArc, IDnum preNodeID,$/;"	f	file:
addPreMarker_pg	preGraph.c	/^PreMarker * addPreMarker_pg(PreGraph * preGraph, IDnum nodeID, IDnum seqID, Coordinate * start, PreMarker * previous) {$/;"	f
addPreNodeToPreGraph_pg	preGraph.c	/^void addPreNodeToPreGraph_pg(PreGraph * preGraph, Coordinate start,$/;"	f
addReadStart	graph.c	/^void addReadStart(Node * node, IDnum seqID, Coordinate position,$/;"	f
addReferenceCoordinate	readSet.c	/^static void addReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {$/;"	f	file:
addUncertainPassageMarker	passageMarker.c	/^PassageMarkerI addUncertainPassageMarker(IDnum sequenceID, Node * node)$/;"	f
adjustLongReads	shortReadPairs.c	/^static void adjustLongReads(Node * target, Node * source)$/;"	f	file:
adjustShortReads	readCoherentGraph.c	/^static void adjustShortReads(Node * target, PassageMarkerI pathMarker)$/;"	f	file:
adjustShortReads	shortReadPairs.c	/^static void adjustShortReads(Node * target, Node * source)$/;"	f	file:
adjustShortReadsByLength	shortReadPairs.c	/^static void adjustShortReadsByLength(Node * target, Coordinate nodeLength)$/;"	f	file:
admitGroupies	readCoherentGraph.c	/^static void admitGroupies(Node * source, Node * bypass)$/;"	f	file:
allocArrayAllocate	allocArray.c	/^allocArrayAllocate (AllocArray *array)$/;"	f
allocArrayFree	allocArray.c	/^allocArrayFree (AllocArray *array, ArrayIdx idx)$/;"	f
allocArrayGetElement	allocArray.c	/^allocArrayGetElement (AllocArray *array, ArrayIdx idx)$/;"	f
allocExitError	utility.c	/^static void allocExitError(const char *function, unsigned long long count,$/;"	f	file:
allocateArc	graph.c	/^Arc *allocateArc()$/;"	f
allocateConnection	scaffold.c	/^static Connection *allocateConnection()$/;"	f	file:
allocateDFibHeapNode	dfib.c	/^static DFibHeapNode *allocateDFibHeapNode(DFibHeap * heap)$/;"	f	file:
allocateFibHeapEl	fib.c	/^static FibHeapNode *allocateFibHeapEl(FibHeap * heap)$/;"	f	file:
allocateGapMarker	graph.c	/^static GapMarker *allocateGapMarker()$/;"	f	file:
allocateKmerOccurences	kmerOccurenceTable.c	/^void allocateKmerOccurences(IDnum kmerCount, KmerOccurenceTable * table) {$/;"	f
allocateNode	graph.c	/^Node *allocateNode()$/;"	f
allocateNodeList	shortReadPairs.c	/^static NodeList *allocateNodeList()$/;"	f	file:
allocateNodeSpace	graph.c	/^void allocateNodeSpace(Graph * graph, IDnum nodeCount)$/;"	f
allocatePassageMarker	passageMarker.c	/^PassageMarkerI allocatePassageMarker()$/;"	f
allocatePassageMarkerList	passageMarker.c	/^PassageMarkerList *allocatePassageMarkerList()$/;"	f
allocatePointer	recycleBin.c	/^void *allocatePointer(RecycleBin * recycle_bin)$/;"	f
allocatePreMarkerCountSpace_pg	preGraph.c	/^void allocatePreMarkerCountSpace_pg(PreGraph * preGraph)$/;"	f
allocatePreMarkerSpace_pg	preGraph.c	/^void allocatePreMarkerSpace_pg(PreGraph * preGraph) {$/;"	f
allocatePreNodeSpace_pg	preGraph.c	/^void allocatePreNodeSpace_pg(PreGraph * preGraph, IDnum preNodeCount)$/;"	f
allocateRBConnection	readCoherentGraph.c	/^static RBConnection *allocateRBConnection()$/;"	f	file:
allocateReadToNodeTables	scaffold.c	/^static ReadOccurence **allocateReadToNodeTables(IDnum * readNodeCounts)$/;"	f	file:
allocateSmallNodeList	graphReConstruction.c	/^static SmallNodeList *allocateSmallNodeList()$/;"	f	file:
allocateSplayNode	splay.c	/^static SplayNode *allocateSplayNode()$/;"	f	file:
annot	preGraphConstruction.c	/^	Annotation *annot;$/;"	m	struct:insertionMarker_st	file:
annotationCount	roadMap.c	/^	ShortLength annotationCount;$/;"	m	struct:roadmap_st	file:
annotation_st	roadMap.c	/^struct annotation_st {$/;"	s	file:
appendDescriptors	graph.c	/^void appendDescriptors(Node * destination, Node * source)$/;"	f
appendDescriptors_pg	preGraph.c	/^void appendDescriptors_pg(Descriptor ** start, int * writeOffset, IDnum preNodeID, PreGraph* preGraph, boolean initial) {$/;"	f
appendGap	graph.c	/^void appendGap(Node * node, Coordinate length, Graph * graph)$/;"	f
appendNegativeDescriptor_pg	preGraph.c	/^static void appendNegativeDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {$/;"	f	file:
appendNodeGaps	graph.c	/^void appendNodeGaps(Node * destination, Node * source, Graph * graph)$/;"	f
appendNodeSequence	graph.c	/^void appendNodeSequence(Node * node, TightString * sequence,$/;"	f
appendPositiveDescriptor_pg	preGraph.c	/^static void appendPositiveDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {$/;"	f	file:
appendSequence	graph.c	/^void appendSequence(Node * node, TightString * reads,$/;"	f
appendSequenceToDescriptor	graph.c	/^static Descriptor *appendSequenceToDescriptor(Descriptor * descr,$/;"	f	file:
arc	graph.c	/^	Arc *arc;		\/\/ 64$/;"	m	struct:node_st	file:
arcCount	graph.c	/^	IDnum arcCount;		\/\/ 32$/;"	m	struct:node_st	file:
arcCount	graph.c	/^int arcCount(Node * node)$/;"	f
arcLookupTable	graph.c	/^	Arc **arcLookupTable;$/;"	m	struct:graph_st	file:
arcMemory	graph.c	/^static RecycleBin *arcMemory = NULL;$/;"	v	file:
arcMergeSort	graph.c	/^static void arcMergeSort(Arc ** arcPtr, IDnum count)$/;"	f	file:
arc_st	graph.c	/^struct arc_st {$/;"	s	file:
array	readSet.c	/^	ReferenceCoordinate * array;$/;"	m	struct:referenceCoordinateTable_st	file:
arrayLength	readSet.c	/^	IDnum arrayLength;$/;"	m	struct:referenceCoordinateTable_st	file:
backReference	shortReadPairs.c	/^	Connection *backReference;$/;"	m	struct:miniConnection_st	file:
blurLastShortReadMarker	graph.c	/^void blurLastShortReadMarker(Node * node, Graph * graph)$/;"	f
buildScaffold	scaffold.c	/^void buildScaffold(Graph * argGraph, ReadSet * reads, boolean * dubious) {$/;"	f
bypass	readCoherentGraph.c	/^static Node *bypass()$/;"	f	file:
callocOrExit3	utility.c	/^void *callocOrExit3(size_t count, size_t size, const char *name)$/;"	f
catDescriptors	graph.c	/^static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength) $/;"	f	file:
categorizeReads	readSet.c	/^void categorizeReads(ReadSet * readSet, Category category)$/;"	f
ceillog2	dfib.c	/^static inline IDnum ceillog2(IDnum a)$/;"	f	file:
ceillog2	fib.c	/^static inline IDnum ceillog2(IDnum a)$/;"	f	file:
chainSawCorrection	graphStats.c	/^void chainSawCorrection(Graph * graph, int minMult)$/;"	f
changeMultiplicity	graph.c	/^void changeMultiplicity(Arc * arc, IDnum variation)$/;"	f
changeMultiplicity_pg	preGraph.c	/^void changeMultiplicity_pg(PreArcI preArc, IDnum variation)$/;"	f
charLeftFilter	kmer.c	/^static const uint8_t charLeftFilter = (uint8_t) 3 << 6; $/;"	v	file:
charToNucleotide	tightString.c	/^Nucleotide charToNucleotide(char c)$/;"	f
charWordFilter	kmer.c	/^static uint8_t charWordFilter = (uint8_t) ((int8_t) -1); $/;"	v	file:
checkNodeForHallidayJunction	graphStats.c	/^static void checkNodeForHallidayJunction(Node * node, Graph * graph)$/;"	f	file:
checkNodeReads	graph.c	/^void checkNodeReads(IDnum index, Graph * graph)$/;"	f
checkPassageMarkersStatus	graph.c	/^void checkPassageMarkersStatus(Graph * graph)$/;"	f
chooseDestination	graphStats.c	/^static Node *chooseDestination(PassageMarkerList * list)$/;"	f	file:
chooseNextInternalPreNode	preGraphConstruction.c	/^static IDnum chooseNextInternalPreNode(IDnum currentPreNodeID,$/;"	f	file:
chunk_list	recycleBin.c	/^	Chunk *chunk_list;$/;"	m	struct:recycleBin_st	file:
chunk_pos	recycleBin.c	/^	int chunk_pos;$/;"	m	struct:recycleBin_st	file:
chunk_st	recycleBin.c	/^typedef struct chunk_st {$/;"	s	file:
cleanMemory	shortReadPairs.c	/^static void cleanMemory()$/;"	f	file:
cleanScaffoldMemory	scaffold.c	/^void cleanScaffoldMemory() {$/;"	f
cleanUpMemory	preGraphConstruction.c	/^cleanUpMemory(PreGraph * preGraph, RoadMapArray * rdmaps, IDnum * chains)$/;"	f	file:
cleanUpNode	graphStats.c	/^static void cleanUpNode(Node * node, Graph * graph)$/;"	f	file:
cleanUpRedundancy	correctedGraph.c	/^static void cleanUpRedundancy()$/;"	f	file:
cleanUpRedundancy_local	locallyCorrectedGraph.c	/^static void cleanUpRedundancy_local()$/;"	f	file:
clearKmer	kmer.c	/^void clearKmer(Kmer * kmer) {$/;"	f
clipNodeLength	graph.c	/^void clipNodeLength(Node * node, Coordinate startClip,$/;"	f
clipTightString	tightString.c	/^void clipTightString(TightString * tString, Coordinate start,$/;"	f
clipTips	correctedGraph.c	/^void clipTips(Graph * graph)$/;"	f
clipTipsHard	correctedGraph.c	/^void clipTipsHard(Graph * graph)$/;"	f
clipTipsVeryHardLocally	locallyCorrectedGraph.c	/^static void clipTipsVeryHardLocally()$/;"	f	file:
clipTips_pg	concatenatedPreGraph.c	/^void clipTips_pg(PreGraph * preGraph)$/;"	f
collectReferenceCoords	graphStats.c	/^static ReferenceCoord * collectReferenceCoords(char * sequencesFilename, IDnum referenceCount) {$/;"	f	file:
comesFromNode	shortReadPairs.c	/^static boolean comesFromNode(PassageMarkerI marker, Node * node)$/;"	f	file:
commonLength	graphStats.c	/^Coordinate commonLength(Node * node, IDnum firstStrain)$/;"	f
commonNodeReads	graph.c	/^ShortReadMarker *commonNodeReads(Node * nodeA, Node * nodeB, Graph * graph,$/;"	f
compareIDnums	graph.c	/^static inline int compareIDnums(const void *A, const void *B)$/;"	f	file:
compareInsertionMarkers	preGraphConstruction.c	/^int compareInsertionMarkers(const void *A, const void *B)$/;"	f
compareKmerOccurences	kmerOccurenceTable.c	/^int compareKmerOccurences(void const *A, void const *B)$/;"	f
compareKmers	kmer.c	/^int compareKmers(Kmer* k1, Kmer* k2) {$/;"	f
compareNodeCovs	graphStats.c	/^int compareNodeCovs(const void * A, const void * B) {$/;"	f
compareNodeMasks	graphReConstruction.c	/^static int compareNodeMasks(const void * ptrA, const void * ptrB) {$/;"	f	file:
comparePaths	correctedGraph.c	/^static void comparePaths(Node * destination, Node * origin)$/;"	f	file:
comparePaths_local	locallyCorrectedGraph.c	/^static void comparePaths_local(Node * destination, Node * origin)$/;"	f	file:
compareReadOccurences	scaffold.c	/^int compareReadOccurences(const void *A, const void * B) {$/;"	f
compareRefCoords	readSet.c	/^static int compareRefCoords(const void * ptrA, const void * ptrB) {$/;"	f	file:
compareRefMaps	graphReConstruction.c	/^static int compareRefMaps(const void * ptrA, const void * ptrB) {$/;"	f	file:
compareReferenceMappings	graphStats.c	/^static int compareReferenceMappings(const void * A, const void * B) {$/;"	f	file:
compareSequences	correctedGraph.c	/^compareSequences(TightString * sequence1, TightString * sequence2)$/;"	f	file:
compareSequences	locallyCorrectedGraph.c	/^compareSequences(TightString * sequence1, TightString * sequence2)$/;"	f	file:
compareShortReadMarkers	graph.c	/^static inline int compareShortReadMarkers(const void *A, const void *B)$/;"	f	file:
computeClearHSPs	splayTable.c	/^static void computeClearHSPs(TightString * array, FILE * seqFile, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum * seqID) {$/;"	f	file:
computeNodeMasks	graphReConstruction.c	/^static NodeMask * computeNodeMasks(ReferenceMapping * referenceMappings, Coordinate arrayLength, Graph * graph) {$/;"	f	file:
computeNodeToNodeMappings	scaffold.c	/^static Connection **computeNodeToNodeMappings(ReadOccurence ** readNodes,$/;"	f	file:
computePartialReadToNodeMapping	scaffold.c	/^static void computePartialReadToNodeMapping(IDnum nodeID,$/;"	f	file:
computeReadToNodeCounts	scaffold.c	/^static IDnum *computeReadToNodeCounts()$/;"	f	file:
computeReadToNodeMappings	scaffold.c	/^static ReadOccurence **computeReadToNodeMappings(IDnum * readNodeCounts, ReadSet * reads)$/;"	f	file:
computeReferenceMappings	graphReConstruction.c	/^static ReferenceMapping * computeReferenceMappings(char * preGraphFilename, ReadSet * reads, Coordinate * referenceMappingLength, IDnum * referenceCount) {$/;"	f	file:
computeSecondInPair	readSet.c	/^static void computeSecondInPair(ReadSet * reads)$/;"	f	file:
computeSubsequentNodesLength	graphStats.c	/^Coordinate computeSubsequentNodesLength(Node * node)$/;"	f
computeVirtualNodeLength	graphStats.c	/^Coordinate computeVirtualNodeLength(Node * node)$/;"	f
concatenateCommonTodoLists	correctedGraph.c	/^static void concatenateCommonTodoLists(Node * nodeA, Node * nodeB)$/;"	f	file:
concatenateGraph	concatenatedGraph.c	/^void concatenateGraph(Graph * graph)$/;"	f
concatenateLongReads	shortReadPairs.c	/^static void concatenateLongReads(Node * node, Node * candidate,$/;"	f	file:
concatenateNodes	concatenatedGraph.c	/^void concatenateNodes(Node * nodeA, Node * nodeB, Graph * graph)$/;"	f
concatenateNodesAndVaccinate	correctedGraph.c	/^static void concatenateNodesAndVaccinate(Node * nodeA, Node * nodeB,$/;"	f	file:
concatenatePassageMarkers	passageMarker.c	/^void concatenatePassageMarkers(PassageMarkerI marker,$/;"	f
concatenatePathNodes	correctedGraph.c	/^static void concatenatePathNodes(PassageMarkerI pathStart)$/;"	f	file:
concatenatePreGraph_pg	concatenatedPreGraph.c	/^void concatenatePreGraph_pg(PreGraph * preGraph)$/;"	f
concatenatePreNodes	concatenatedPreGraph.c	/^static void concatenatePreNodes(IDnum preNodeAID, $/;"	f	file:
concatenateReadSets	readSet.c	/^void concatenateReadSets(ReadSet * A, ReadSet * B)$/;"	f
concatenateReadStarts	concatenatedGraph.c	/^void concatenateReadStarts(Node * target, Node * source, Graph * graph)$/;"	f
concatenateReferenceMarkers_H2H_pg	preGraph.c	/^static void concatenateReferenceMarkers_H2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;"	f	file:
concatenateReferenceMarkers_H2T_pg	preGraph.c	/^static void concatenateReferenceMarkers_H2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;"	f	file:
concatenateReferenceMarkers_T2H_pg	preGraph.c	/^static void concatenateReferenceMarkers_T2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;"	f	file:
concatenateReferenceMarkers_T2T_pg	preGraph.c	/^static void concatenateReferenceMarkers_T2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;"	f	file:
concatenateReferenceMarkers_pg	preGraph.c	/^void concatenateReferenceMarkers_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;"	f
concatenateStringOfNodes	concatenatedGraph.c	/^void concatenateStringOfNodes(Node * nodeA, Graph * graph)$/;"	f
concatenateTightStringArrays	tightString.c	/^TightString **concatenateTightStringArrays(TightString ** array1,$/;"	f
concatenateTodoListIntoActive	correctedGraph.c	/^static void concatenateTodoListIntoActive(Node * nodeB)$/;"	f	file:
concatenateTodoLists	correctedGraph.c	/^static void concatenateTodoLists(Node * nodeA, Node * nodeB)$/;"	f	file:
connectAnnotation	preGraphConstruction.c	/^static void connectAnnotation(IDnum * currentPreNodeID, Annotation * annot,$/;"	f	file:
connectDomain	graphStats.c	/^static Coordinate connectDomain(Node * node)$/;"	f	file:
connectDomainNodeCount	graphStats.c	/^static Coordinate connectDomainNodeCount(Node * node)$/;"	f	file:
connectPassageMarkers	passageMarker.c	/^connectPassageMarkers(PassageMarkerI previous, PassageMarkerI next,$/;"	f
connectPreNodeToTheNext	preGraphConstruction.c	/^static void connectPreNodeToTheNext(IDnum * currentPreNodeID,$/;"	f	file:
connectPreNodes	preGraphConstruction.c	/^static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
connectionMemory	scaffold.c	/^static RecycleBin *connectionMemory = NULL;$/;"	v	file:
connection_st	scaffold.c	/^struct connection_st {$/;"	s	file:
contigStats	graphStats.c	/^void contigStats(Node ** contigs, IDnum readCount)$/;"	f
convertConfidenceScores	readSet.c	/^void convertConfidenceScores(ReadSet * rs, int WORDLENGTH)$/;"	f
convertInsertionMarkers	preGraphConstruction.c	/^static void convertInsertionMarkers(InsertionMarker * insertionMarkers,$/;"	f	file:
convertMarker	preGraphConstruction.c	/^static void convertMarker(InsertionMarker * marker, IDnum nodeID)$/;"	f	file:
convertQualityScore	readSet.c	/^static Probability convertQualityScore(Quality score)$/;"	f	file:
convertSequences	readSet.c	/^void convertSequences(ReadSet * rs)$/;"	f
coord	roadMap.c	/^	IDnum coord;$/;"	m	union:positionPtr	file:
copyDownDescriptor	graph.c	/^static void copyDownDescriptor(Descriptor ** writePtr, int *writeOffset,$/;"	f	file:
copyDownSequence	graph.c	/^static void copyDownSequence(Descriptor ** writePtr, int *writeOffset,$/;"	f	file:
copyKmers	kmer.c	/^void copyKmers(Kmer* k1, Kmer* k2) {$/;"	f
copyMarkers	graphStats.c	/^static PassageMarkerList *copyMarkers(Node * node)$/;"	f	file:
copyPassageMarker	passageMarker.c	/^PassageMarkerI copyPassageMarker(PassageMarkerI marker)$/;"	f
copyPassageMarkerList	passageMarker.c	/^PassageMarkerList *copyPassageMarkerList(PassageMarkerList * list)$/;"	f
copyPreMarker	preGraph.c	/^static void copyPreMarker(PreMarker * dest, PreMarker * source, IDnum preNodeAID, PreGraph * preGraph) {$/;"	f	file:
correctGraph	correctedGraph.c	/^void correctGraph(Graph * argGraph, IDnum * argSequenceLengths, Category * argSequenceCategories)$/;"	f
correctGraphLocally	locallyCorrectedGraph.c	/^void correctGraphLocally(Node * argStart)$/;"	f
countBreakpoints	graphStats.c	/^IDnum countBreakpoints(Graph * graph, IDnum firstStrain)$/;"	f
countCoOccurences	scaffold.c	/^static boolean * countCoOccurences(IDnum * coOccurencesCount, ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {$/;"	f	file:
countCommonLength	graphStats.c	/^Coordinate countCommonLength(Graph * graph, IDnum firstStrain)$/;"	f
countLocalBreakpoints	graphStats.c	/^int countLocalBreakpoints(PassageMarkerI marker, IDnum firstStrain)$/;"	f
countMappings	graphReConstruction.c	/^static IDnum countMappings(char * preGraphFilename) {$/;"	f	file:
countOccurenceInSplayTree	splay.c	/^void countOccurenceInSplayTree(Kmer * kmer, SplayTree ** T, int increment)$/;"	f
countPreNodes	preGraphConstruction.c	/^countPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
countReferenceKmers	splayTable.c	/^static Coordinate countReferenceKmers(ReadSet * reads, int wordLength) {$/;"	f	file:
countRepeats	graphStats.c	/^IDnum countRepeats(Graph * graph)$/;"	f
countSNPs	graphStats.c	/^IDnum countSNPs(Graph * graph, IDnum firstStrain, int WORDLENGTH)$/;"	f
countShortReads	scaffold.c	/^static IDnum **countShortReads(Graph * graph, ReadSet * reads)$/;"	f	file:
countSinksAndSources	graphStats.c	/^IDnum countSinksAndSources(Graph * graph)$/;"	f
countStrainOnlyBp	graphStats.c	/^Coordinate countStrainOnlyBp(Graph * graph, IDnum firstStrain)$/;"	f
countStrainOnlyNodes	graphStats.c	/^IDnum countStrainOnlyNodes(Graph * graph, IDnum firstStrain)$/;"	f
countTangles	graphStats.c	/^IDnum countTangles(Graph * graph)$/;"	f
crc32_v	crc.c	/^int crc32_v(const char *buf, int len)$/;"	f
crc_table	crc.c	/^static int crc_table[256] = {$/;"	v	file:
createAnalogousArc	graph.c	/^void createAnalogousArc(Node * originNode, Node * destinationNode,$/;"	f
createAnalogousArcAndVaccinate	correctedGraph.c	/^static void createAnalogousArcAndVaccinate(Node * nodeA, Node * nodeB,$/;"	f	file:
createAnalogousPreArc_pg	preGraph.c	/^void createAnalogousPreArc_pg(IDnum originPreNodeID,$/;"	f
createArc	graph.c	/^Arc *createArc(Node * originNode, Node * destinationNode, Graph * graph)$/;"	f
createConnection	scaffold.c	/^static void createConnection(IDnum nodeID, IDnum node2ID,$/;"	f	file:
createNewConnection	scaffold.c	/^Connection *createNewConnection(IDnum nodeID, IDnum node2ID,$/;"	f
createNodeLocks	graphReConstruction.c	/^createNodeLocks(Graph *graph)$/;"	f	file:
createNodeReadStartArrays	graph.c	/^void createNodeReadStartArrays(Graph * graph)$/;"	f
createOwnerThreads	graphReConstruction.c	/^createOwnerThreads(Graph *graph)$/;"	f	file:
createPreArc_pg	preGraph.c	/^PreArcI createPreArc_pg(IDnum originPreNodeID, IDnum destinationPreNodeID,$/;"	f
createPreMarkers	preGraphConstruction.c	/^static void createPreMarkers(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
createPreNodes	preGraphConstruction.c	/^createPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
createReadPairingArray	readSet.c	/^void createReadPairingArray(ReadSet* reads) {$/;"	f
createTwinConnection	scaffold.c	/^static void createTwinConnection(IDnum nodeID, IDnum node2ID,$/;"	f	file:
dbgCounter	correctedGraph.c	/^static IDnum dbgCounter;$/;"	v	file:
dbgCounter	readCoherentGraph.c	/^static IDnum dbgCounter = 0;$/;"	v	file:
deactivateArcLookupTable	graph.c	/^void deactivateArcLookupTable(Graph * graph)$/;"	f
deactivateGapMarkers	graph.c	/^void deactivateGapMarkers(Graph * graph)$/;"	f
deactivateLocalCorrectionSettings	locallyCorrectedGraph.c	/^void deactivateLocalCorrectionSettings()$/;"	f
deactivateReadStarts	graph.c	/^void deactivateReadStarts(Graph * graph)$/;"	f
deallocateArc	graph.c	/^void deallocateArc(Arc * arc)$/;"	f
deallocateConnection	scaffold.c	/^static void deallocateConnection(Connection * connect)$/;"	f	file:
deallocateDFibHeapNode	dfib.c	/^static void deallocateDFibHeapNode(DFibHeapNode * a, DFibHeap * heap)$/;"	f	file:
deallocateFibHeapEl	fib.c	/^static void deallocateFibHeapEl(FibHeapNode * a, FibHeap * heap)$/;"	f	file:
deallocateNode	graph.c	/^void deallocateNode(Node * node)$/;"	f
deallocateNodeList	shortReadPairs.c	/^static void deallocateNodeList(NodeList * nodeList)$/;"	f	file:
deallocatePassageMarker	passageMarker.c	/^static void deallocatePassageMarker(PassageMarkerI marker)$/;"	f	file:
deallocatePassageMarkerList	passageMarker.c	/^void deallocatePassageMarkerList(PassageMarkerList * marker)$/;"	f
deallocatePointer	recycleBin.c	/^void deallocatePointer(RecycleBin * recycle_bin, void *data)$/;"	f
deallocatePreArc_pg	preGraph.c	/^void deallocatePreArc_pg(PreArcI preArc)$/;"	f
deallocateRBConnection	readCoherentGraph.c	/^static void deallocateRBConnection(RBConnection * nodeList)$/;"	f	file:
deallocateSmallNodeList	graphReConstruction.c	/^static void deallocateSmallNodeList(SmallNodeList * smallNodeList)$/;"	f	file:
deallocateSplayNode	splay.c	/^static void deallocateSplayNode(SplayNode * node)$/;"	f	file:
descriptor	graph.c	/^	Descriptor *descriptor;	\/\/ 64$/;"	m	struct:node_st	file:
descriptor	preGraph.c	/^	Descriptor *descriptor;$/;"	m	struct:preNode_st	file:
destination	graph.c	/^	Node *destination;	\/\/ 64$/;"	m	struct:arc_st	file:
destination	scaffold.c	/^	Node *destination;$/;"	m	struct:connection_st	file:
destroyAllPassageMarkers	passageMarker.c	/^void destroyAllPassageMarkers()$/;"	f
destroyAllSplayTrees	splay.c	/^void destroyAllSplayTrees()$/;"	f
destroyAllocArray	allocArray.c	/^destroyAllocArray (AllocArray *array)$/;"	f
destroyArc	graph.c	/^void destroyArc(Arc * arc, Graph * graph)$/;"	f
destroyConnectedDomain	graphStats.c	/^static void destroyConnectedDomain(Node * node, Graph * graph)$/;"	f	file:
destroyConnection	scaffold.c	/^void destroyConnection(Connection * connect, IDnum nodeID)$/;"	f
destroyDHeap	dfibHeap.c	/^void destroyDHeap(DFibHeap * heap)$/;"	f
destroyDisconnectedElements	graphStats.c	/^void destroyDisconnectedElements(Graph * graph)$/;"	f
destroyEmptyNodes	graphStats.c	/^void destroyEmptyNodes(Graph * graph)$/;"	f
destroyGraph	graph.c	/^void destroyGraph(Graph * graph)$/;"	f
destroyHeap	fibHeap.c	/^void destroyHeap(FibHeap * heap)$/;"	f
destroyKmerOccurenceTable	kmerOccurenceTable.c	/^void destroyKmerOccurenceTable(KmerOccurenceTable * kmerTable) {$/;"	f
destroyMixedNode	graphStats.c	/^static void destroyMixedNode(Node * node)$/;"	f	file:
destroyMixedReads	graphStats.c	/^void destroyMixedReads(Graph * graph, IDnum minCoverage)$/;"	f
destroyNode	graph.c	/^void destroyNode(Node * node, Graph * graph)$/;"	f
destroyNodeInDHeap	dfibHeap.c	/^void destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap)$/;"	f
destroyNodeInHeap	fibHeap.c	/^void destroyNodeInHeap(FibHeapNode * node, FibHeap * heap)$/;"	f
destroyNodeList	shortReadPairs.c	/^static void destroyNodeList(NodeList * nodeList)$/;"	f	file:
destroyPassageMarker	passageMarker.c	/^void destroyPassageMarker(PassageMarkerI marker)$/;"	f
destroyPassageMarkerList	correctedGraph.c	/^static void destroyPassageMarkerList(PassageMarkerList ** list)$/;"	f	file:
destroyPassageMarkerList	graphStats.c	/^static void destroyPassageMarkerList(PassageMarkerList ** list)$/;"	f	file:
destroyPaths	correctedGraph.c	/^static void destroyPaths()$/;"	f	file:
destroyPaths	locallyCorrectedGraph.c	/^static void destroyPaths()$/;"	f	file:
destroyPreArc_pg	preGraph.c	/^void destroyPreArc_pg(PreArcI preArc, PreGraph * preGraph)$/;"	f
destroyPreGraph_pg	preGraph.c	/^void destroyPreGraph_pg(PreGraph * preGraph)$/;"	f
destroyPreNode_pg	preGraph.c	/^void destroyPreNode_pg(IDnum preNodeID, PreGraph * preGraph)$/;"	f
destroyRead	graphStats.c	/^static void destroyRead(PassageMarkerI marker)$/;"	f	file:
destroyReadSet	readSet.c	/^void destroyReadSet(ReadSet * reads)$/;"	f
destroyRecycleBin	recycleBin.c	/^void destroyRecycleBin(RecycleBin * recycleBin)$/;"	f
destroyRecycleBinArray	recycleBin.c	/^void destroyRecycleBinArray(RecycleBin * recycleBin)$/;"	f
destroyRecycleBinChunks	recycleBin.c	/^static void destroyRecycleBinChunks(RecycleBin * recycleBin)$/;"	f	file:
destroyReferenceCoordinateTable	readSet.c	/^static void destroyReferenceCoordinateTable(ReferenceCoordinateTable * table) {$/;"	f	file:
destroyRoadMapArray	roadMap.c	/^void destroyRoadMapArray(RoadMapArray * rdmaps) {$/;"	f
destroyShortTips	graphStats.c	/^void destroyShortTips(Graph * graph)$/;"	f
destroySinglePoolNodes	graphStats.c	/^void destroySinglePoolNodes(Graph * graph)$/;"	f
destroySinglePoolNodesStrict	graphStats.c	/^void destroySinglePoolNodesStrict(Graph * graph)$/;"	f
destroySplayTable	splayTable.c	/^void destroySplayTable(SplayTable * splayTable)$/;"	f
destroySplayTree	splay.c	/^void destroySplayTree(SplayTree * T)$/;"	f
destroyStrainSpecificIslands	graphStats.c	/^void destroyStrainSpecificIslands(Graph * graph, IDnum firstStrain)$/;"	f
destroyTightString	tightString.c	/^void destroyTightString(TightString * tString)$/;"	f
destroyTightStringArray	tightString.c	/^void destroyTightStringArray(TightString ** array, IDnum sequenceCount)$/;"	f
destroyWholeRead	graphStats.c	/^static void destroyWholeRead(PassageMarkerI marker)$/;"	f	file:
detachDubiousReads	readSet.c	/^void detachDubiousReads(ReadSet * reads, boolean * dubiousReads)$/;"	f
detachImprobablePairs	shortReadPairs.c	/^void detachImprobablePairs(ReadSet * sequences)$/;"	f
determineEligibleStartingPoints	correctedGraph.c	/^static void determineEligibleStartingPoints()$/;"	f	file:
dfh_cascading_cut	dfib.c	/^static void dfh_cascading_cut(DFibHeap * h, DFibHeapNode * y)$/;"	f	file:
dfh_checkcons	dfib.c	/^static void dfh_checkcons(DFibHeap * h)$/;"	f	file:
dfh_compare	dfib.c	/^static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b)$/;"	f	file:
dfh_comparedata	dfib.c	/^dfh_comparedata(DFibHeap * h, Time key, void *data, DFibHeapNode * b)$/;"	f	file:
dfh_consolidate	dfib.c	/^static void dfh_consolidate(DFibHeap * h)$/;"	f	file:
dfh_cut	dfib.c	/^static void dfh_cut(DFibHeap * h, DFibHeapNode * x, DFibHeapNode * y)$/;"	f	file:
dfh_delete	dfib.c	/^void *dfh_delete(DFibHeap * h, DFibHeapNode * x)$/;"	f
dfh_deleteheap	dfib.c	/^void dfh_deleteheap(DFibHeap * h)$/;"	f
dfh_extractmin	dfib.c	/^void *dfh_extractmin(DFibHeap * h)$/;"	f
dfh_extractminel	dfib.c	/^static DFibHeapNode *dfh_extractminel(DFibHeap * h)$/;"	f	file:
dfh_heaplink	dfib.c	/^static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x)$/;"	f	file:
dfh_insertel	dfib.c	/^static void dfh_insertel(DFibHeap * h, DFibHeapNode * x)$/;"	f	file:
dfh_insertkey	dfib.c	/^DFibHeapNode *dfh_insertkey(DFibHeap * h, Time key, void *data)$/;"	f
dfh_insertrootlist	dfib.c	/^static void dfh_insertrootlist(DFibHeap * h, DFibHeapNode * x)$/;"	f	file:
dfh_makekeyheap	dfib.c	/^DFibHeap *dfh_makekeyheap()$/;"	f
dfh_removerootlist	dfib.c	/^static void dfh_removerootlist(DFibHeap * h, DFibHeapNode * x)$/;"	f	file:
dfh_replacedata	dfib.c	/^void *dfh_replacedata(DFibHeapNode * x, void *data)$/;"	f
dfh_replacekey	dfib.c	/^Time dfh_replacekey(DFibHeap * h, DFibHeapNode * x, Time key)$/;"	f
dfh_replacekeydata	dfib.c	/^void *dfh_replacekeydata(DFibHeap * h, DFibHeapNode * x,$/;"	f
dfhe_insertafter	dfib.c	/^static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b)$/;"	f	file:
dfhe_insertbefore	dfib.c	/^static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b)$/;"	f	file:
dfhe_newelem	dfib.c	/^static DFibHeapNode *dfhe_newelem(DFibHeap * h)$/;"	f	file:
dfhe_remove	dfib.c	/^static DFibHeapNode *dfhe_remove(DFibHeapNode * x)$/;"	f	file:
dfibheap_el_getKey	dfib.c	/^Time dfibheap_el_getKey(DFibHeapNode * node)$/;"	f
dfibheap_getSize	dfib.c	/^IDnum dfibheap_getSize(DFibHeap * heap)$/;"	f
dheap	correctedGraph.c	/^static DFibHeap *dheap;$/;"	v	file:
dheap	locallyCorrectedGraph.c	/^static DFibHeap *dheap;$/;"	v	file:
dheapNodes	correctedGraph.c	/^static DFibHeapNode **dheapNodes;$/;"	v	file:
dheapNodes	locallyCorrectedGraph.c	/^static DFibHeapNode **dheapNodes;$/;"	v	file:
direct_count	scaffold.c	/^	IDnum direct_count;$/;"	m	struct:connection_st	file:
directlyAppendDescriptors	graph.c	/^void directlyAppendDescriptors(Node * destination, Node * source, Coordinate totalLength)$/;"	f
disconnectNextPassageMarker	passageMarker.c	/^void disconnectNextPassageMarker(PassageMarkerI marker, Graph * graph)$/;"	f
displayArcMemory	graph.c	/^void displayArcMemory()$/;"	f
displayBreakpoints	graphStats.c	/^void displayBreakpoints(Graph * graph, IDnum firstStrain)$/;"	f
displayGeneralStatistics	graphStats.c	/^void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads)$/;"	f
displayGraph	graph.c	/^void displayGraph(Graph * graph)$/;"	f
displayGraphStatistics	graphStats.c	/^void displayGraphStatistics(Graph * graph)$/;"	f
displayGraphStatisticsSelective	graphStats.c	/^void displayGraphStatisticsSelective(Graph * graph, IDnum first)$/;"	f
displayLocalBreakpoint	graphStats.c	/^void displayLocalBreakpoint(PassageMarkerI strainMarker,$/;"	f
displayNodeMemory	graph.c	/^void displayNodeMemory()$/;"	f
displayNodeStatisticsSelective	graphStats.c	/^void displayNodeStatisticsSelective(Node * node, IDnum first)$/;"	f
displayPreArcMemory_pg	preGraph.c	/^void displayPreArcMemory_pg()$/;"	f
displaySplayTreeMemory	splay.c	/^void displaySplayTreeMemory()$/;"	f
displayStrainOnlyDescriptors	graphStats.c	/^void displayStrainOnlyDescriptors(Graph * graph, IDnum firstStrain)$/;"	f
displayStrainOnlySequences	graphStats.c	/^void displayStrainOnlySequences(Graph * graph, IDnum firstStrain,$/;"	f
distance	scaffold.c	/^	double distance;$/;"	m	struct:connection_st	file:
distance	shortReadPairs.c	/^	IDnum distance;$/;"	m	struct:miniConnection_st	file:
doFindOrInsertOccurenceInSplayTree	splayTable.c	/^doFindOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,$/;"	f	file:
done	correctedGraph.c	/^static Ticket *done;$/;"	v	file:
doubleStrandedGraph	graph.c	/^boolean doubleStrandedGraph(Graph * graph) {$/;"	f
double_strand	preGraph.c	/^	boolean double_strand;$/;"	m	struct:preGraph_st	file:
double_strand	splayTable.c	/^	boolean double_strand;$/;"	m	struct:splayTable_st	file:
double_stranded	graph.c	/^	boolean double_stranded;$/;"	m	struct:graph_st	file:
eligibleStartingPoints	correctedGraph.c	/^static IDnum *eligibleStartingPoints;$/;"	v	file:
emptyGraph	graph.c	/^Graph *emptyGraph(IDnum sequenceCount, int wordLength)$/;"	f
emptyNode	graph.c	/^Node *emptyNode()$/;"	f
emptyPreGraph_pg	preGraph.c	/^PreGraph *emptyPreGraph_pg(IDnum sequenceCount, IDnum referenceCount, int wordLength, boolean double_strand)$/;"	f
estimateLibraryInsertLength	scaffold.c	/^static void estimateLibraryInsertLength(Coordinate * coOccurences, IDnum coOccurencesCount, Category libID) {$/;"	f	file:
estimateLibraryInsertLengths	scaffold.c	/^static void estimateLibraryInsertLengths(Coordinate ** coOccurences, IDnum * coOccurencesCounts) {$/;"	f	file:
estimateMissingInsertLengths	scaffold.c	/^static void estimateMissingInsertLengths(ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {$/;"	f	file:
estimated	scaffold.c	/^static boolean estimated[CATEGORIES + 1];$/;"	v	file:
estimated_cov	graphStats.c	/^double estimated_cov(Graph * graph, char * directory)$/;"	f
exitErrorf	utility.c	/^void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)$/;"	f
expandLongNode	shortReadPairs.c	/^static boolean expandLongNode(Node * node, boolean force_jumps)$/;"	f	file:
expandLongNodes	shortReadPairs.c	/^static boolean expandLongNodes(boolean force_jumps)$/;"	f	file:
expandNode	graph.c	/^TightString *expandNode(Node * node, int WORDLENGTH)$/;"	f
expandNodeFragment	graph.c	/^char *expandNodeFragment(Node * node, Coordinate contigStart,$/;"	f
expandPassageMarker	sequenceExpander.c	/^TightString *expandPassageMarker(PassageMarkerI marker,$/;"	f
expectedNumberOfConnections	scaffold.c	/^static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,$/;"	f	file:
expected_coverage	readCoherentGraph.c	/^static double expected_coverage = 1;$/;"	v	file:
exploitShortReadPairs	shortReadPairs.c	/^void exploitShortReadPairs(Graph * argGraph, ReadSet * reads,$/;"	f
exportAMOSContig	graphStats.c	/^static void exportAMOSContig(FILE * outfile, ReadSet * reads, Node * node,$/;"	f	file:
exportAMOSContigs	graphStats.c	/^void exportAMOSContigs(char *filename, Graph * graph,$/;"	f
exportAMOSLib	graphStats.c	/^static void exportAMOSLib(FILE * outfile, Graph * graph, Category cat)$/;"	f	file:
exportAMOSMarker	graphStats.c	/^static void exportAMOSMarker(FILE * outfile, PassageMarkerI marker,$/;"	f	file:
exportAMOSNode	graphStats.c	/^static void exportAMOSNode(FILE * outfile, ReadSet * reads, Node * node,$/;"	f	file:
exportAMOSRead	graphStats.c	/^static void exportAMOSRead(FILE * outfile, TightString * tString,$/;"	f	file:
exportAMOSReverseShortMarker	graphStats.c	/^static void exportAMOSReverseShortMarker(FILE * outfile,$/;"	f	file:
exportAMOSShortMarker	graphStats.c	/^static void exportAMOSShortMarker(FILE * outfile, ShortReadMarker * marker,$/;"	f	file:
exportArc	graph.c	/^static void exportArc(FILE * outfile, Arc * arc)$/;"	f	file:
exportArcSequence	graphStats.c	/^void exportArcSequence(Arc * arc, FILE * outfile, int WORDLENGTH,$/;"	f
exportContigs	graphStats.c	/^void exportContigs(Node ** contigs, ReadSet * reads, char *filename,$/;"	f
exportDOTGraph	graph.c	/^void exportDOTGraph(char *filename, Graph * graph)$/;"	f
exportGraph	graph.c	/^void exportGraph(char *filename, Graph * graph, TightString * sequences)$/;"	f
exportIDMapping	readSet.c	/^void exportIDMapping(char *filename, ReadSet * reads)$/;"	f
exportLongNodeMapping	graphStats.c	/^static void exportLongNodeMapping(FILE * outfile, Node * node, ReadSet * reads, ReferenceCoord * refCoords, int wordLength) {$/;"	f	file:
exportLongNodeMappings	graphStats.c	/^void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,$/;"	f
exportLongNodeSequences	graphStats.c	/^void exportLongNodeSequences(char *filename, Graph * graph,$/;"	f
exportMarker	passageMarker.c	/^void exportMarker(FILE * outfile, PassageMarkerI marker,$/;"	f
exportNode	graph.c	/^static void exportNode(FILE * outfile, Node * node, void *withSequence)$/;"	f	file:
exportPreGraph_pg	preGraph.c	/^void exportPreGraph_pg(char *filename, PreGraph * preGraph)$/;"	f
exportPreMarker	preGraph.c	/^static void exportPreMarker(FILE * outfile, PreMarker* preMarker) {$/;"	f	file:
exportPreNode_pg	preGraph.c	/^static void exportPreNode_pg(FILE * outfile, PreNode * preNode, IDnum ID,$/;"	f	file:
exportPreReference_pg	preGraph.c	/^static void exportPreReference_pg(FILE * outfile, IDnum index, PreGraph * preGraph) {$/;"	f	file:
exportRead	readSet.c	/^static void exportRead(FILE * outfile, ReadSet * reads, IDnum index)$/;"	f	file:
exportReadSet	readSet.c	/^void exportReadSet(char *filename, ReadSet * reads)$/;"	f
exportSequenceArray	tightString.c	/^void exportSequenceArray(char *filename, TightString ** array,$/;"	f
exportTightString	tightString.c	/^void exportTightString(FILE * outfile, TightString * sequence, IDnum index)$/;"	f
exportUnusedReads	graphStats.c	/^void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLength, char* directory) {$/;"	f
extractBackOfNodeReads	graph.c	/^ShortReadMarker *extractBackOfNodeReads(Node * node, Coordinate breakpoint,$/;"	f
extractFrontOfNodeReads	graph.c	/^ShortReadMarker *extractFrontOfNodeReads(Node * node,$/;"	f
extractPassageMarker	passageMarker.c	/^void extractPassageMarker(PassageMarkerI marker)$/;"	f
extractSequence	correctedGraph.c	/^extractSequence(PassageMarkerI path, TightString * sequence)$/;"	f	file:
extractSequence	locallyCorrectedGraph.c	/^extractSequence(PassageMarkerI path, TightString * sequence)$/;"	f	file:
fastPath	correctedGraph.c	/^static PassageMarkerI fastPath;$/;"	v	file:
fastPath	locallyCorrectedGraph.c	/^static PassageMarkerI fastPath;$/;"	v	file:
fastSequence	correctedGraph.c	/^static TightString *fastSequence;$/;"	v	file:
fastSequence	locallyCorrectedGraph.c	/^static TightString *fastSequence;$/;"	v	file:
fastToSlowMapping	correctedGraph.c	/^static Coordinate *fastToSlowMapping;$/;"	v	file:
fh_cascading_cut	fib.c	/^static void fh_cascading_cut(FibHeap * h, FibHeapNode * y)$/;"	f	file:
fh_checkcons	fib.c	/^static void fh_checkcons(FibHeap * h)$/;"	f	file:
fh_compare	fib.c	/^static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b)$/;"	f	file:
fh_comparedata	fib.c	/^fh_comparedata(FibHeap * h, Coordinate key, void *data, FibHeapNode * b)$/;"	f	file:
fh_consolidate	fib.c	/^static void fh_consolidate(FibHeap * h)$/;"	f	file:
fh_cut	fib.c	/^static void fh_cut(FibHeap * h, FibHeapNode * x, FibHeapNode * y)$/;"	f	file:
fh_delete	fib.c	/^void *fh_delete(FibHeap * h, FibHeapNode * x)$/;"	f
fh_deleteheap	fib.c	/^void fh_deleteheap(FibHeap * h)$/;"	f
fh_destroyheap	fib.c	/^static void fh_destroyheap(FibHeap * h)$/;"	f	file:
fh_extractmin	fib.c	/^void *fh_extractmin(FibHeap * h)$/;"	f
fh_extractminel	fib.c	/^static FibHeapNode *fh_extractminel(FibHeap * h)$/;"	f	file:
fh_heaplink	fib.c	/^static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x)$/;"	f	file:
fh_initheap	fib.c	/^static void fh_initheap(FibHeap * new)$/;"	f	file:
fh_insert	fib.c	/^FibHeapNode *fh_insert(FibHeap * h, void *data)$/;"	f
fh_insertel	fib.c	/^static void fh_insertel(FibHeap * h, FibHeapNode * x)$/;"	f	file:
fh_insertkey	fib.c	/^FibHeapNode *fh_insertkey(FibHeap * h, Coordinate key, void *data)$/;"	f
fh_insertrootlist	fib.c	/^static void fh_insertrootlist(FibHeap * h, FibHeapNode * x)$/;"	f	file:
fh_makeheap	fib.c	/^FibHeap *fh_makeheap()$/;"	f
fh_makekeyheap	fib.c	/^FibHeap *fh_makekeyheap()$/;"	f
fh_min	fib.c	/^void *fh_min(FibHeap * h)$/;"	f
fh_minkey	fib.c	/^Coordinate fh_minkey(FibHeap * h)$/;"	f
fh_removerootlist	fib.c	/^static void fh_removerootlist(FibHeap * h, FibHeapNode * x)$/;"	f	file:
fh_replacedata	fib.c	/^void *fh_replacedata(FibHeapNode * x, void *data)$/;"	f
fh_replacekey	fib.c	/^Coordinate fh_replacekey(FibHeap * h, FibHeapNode * x, Coordinate key)$/;"	f
fh_replacekeydata	fib.c	/^void *fh_replacekeydata(FibHeap * h, FibHeapNode * x,$/;"	f
fh_setcmp	fib.c	/^voidcmp fh_setcmp(FibHeap * h, voidcmp fnct)$/;"	f
fh_setneginf	fib.c	/^void *fh_setneginf(FibHeap * h, void *data)$/;"	f
fh_union	fib.c	/^FibHeap *fh_union(FibHeap * ha, FibHeap * hb)$/;"	f
fhe_initelem	fib.c	/^static void fhe_initelem(FibHeapNode * e)$/;"	f	file:
fhe_insertafter	fib.c	/^static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b)$/;"	f	file:
fhe_insertbefore	fib.c	/^static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b)$/;"	f	file:
fhe_newelem	fib.c	/^static FibHeapNode *fhe_newelem(FibHeap * h)$/;"	f	file:
fhe_remove	fib.c	/^static FibHeapNode *fhe_remove(FibHeapNode * x)$/;"	f	file:
fillReferenceCoordinateTable	readSet.c	/^static void fillReferenceCoordinateTable(char *filename, ReferenceCoordinateTable * refCoords, IDnum counter)$/;"	f	file:
fillTightStringWithString	tightString.c	/^static void fillTightStringWithString(TightString * tString,$/;"	f	file:
fillUpGraph	graphReConstruction.c	/^static void fillUpGraph(ReadSet * reads,$/;"	f	file:
filterAndExportSplayTree	splay.c	/^void filterAndExportSplayTree(FILE * file, SplayTree * T, int minCov,$/;"	f
findConnection	scaffold.c	/^static Connection *findConnection(IDnum nodeID, IDnum node2ID)$/;"	f	file:
findIDnumInArray	graph.c	/^boolean findIDnumInArray(IDnum query, IDnum * array, IDnum arrayLength)$/;"	f
findInTree	splay.c	/^Kmer * findInTree(Kmer * X, SplayTree ** T)$/;"	f
findKmerInKmerOccurenceTable	kmerOccurenceTable.c	/^KmerOccurence *findKmerInKmerOccurenceTable(Kmer * kmer,$/;"	f
findOppositeNode	shortReadPairs.c	/^static void findOppositeNode(Node * node, Node ** oppositeNode,$/;"	f	file:
findOrInsertOccurenceInSplayTable	splayTable.c	/^static boolean findOrInsertOccurenceInSplayTable(Kmer * kmer, IDnum * seqID,$/;"	f	file:
findOrInsertOccurenceInSplayTree	splay.c	/^findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,$/;"	f
findReferenceCoordinate	readSet.c	/^static ReferenceCoordinate * findReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {$/;"	f	file:
findReferenceMapping	graphReConstruction.c	/^static ReferenceMapping * findReferenceMapping(IDnum seqID, Coordinate refCoord, ReferenceMapping * referenceMappings, Coordinate referenceMappingCount) {$/;"	f	file:
finish	graphReConstruction.c	/^	IDnum finish;$/;"	m	struct:nodeMask_st	file:
finish	graphStats.c	/^	IDnum finish;$/;"	m	struct:refMap_st	file:
finish	graphStats.c	/^	IDnum finish;$/;"	m	struct:referenceCoord_st	file:
finish	readSet.c	/^	Coordinate finish;$/;"	m	struct:referenceCoordinate_st	file:
finish	roadMap.c	/^	union positionPtr finish;	\/\/ 32$/;"	m	struct:annotation_st	typeref:union:annotation_st::positionPtr	file:
finishOffset	passageMarker.c	/^	IDnum finishOffset;$/;"	m	struct:passage_st	file:
foldSymmetricalNode	correctedGraph.c	/^static void foldSymmetricalNode(Node * node)$/;"	f	file:
foldSymmetricalNodeReads	graph.c	/^void foldSymmetricalNodeReads(Node * node, Graph * graph)$/;"	f
followShortPath	graphStats.c	/^static Node *followShortPath(Arc * arc)$/;"	f	file:
fprintfReferenceMapping	graphStats.c	/^static void fprintfReferenceMapping(FILE * file, ReferenceMapping * mapping, ReferenceCoord * refCoords, int wordLength) {$/;"	f	file:
freeDoneTickets	correctedGraph.c	/^static void freeDoneTickets()$/;"	f	file:
frontReference	shortReadPairs.c	/^	Connection *frontReference;$/;"	m	struct:miniConnection_st	file:
gapMarkerMemory	graph.c	/^static RecycleBin *gapMarkerMemory = NULL;$/;"	v	file:
gapMarker_st	graph.c	/^struct gapMarker_st {$/;"	s	file:
gapMarkers	graph.c	/^	GapMarker **gapMarkers;$/;"	m	struct:graph_st	file:
gapMergeSort	graph.c	/^static void gapMergeSort(GapMarker ** gapPtr, IDnum count)$/;"	f	file:
genomeMarker	graphStats.c	/^PassageMarkerI genomeMarker(Node * node, IDnum firstStrain)$/;"	f
genomeMarkerCount	graphStats.c	/^IDnum genomeMarkerCount(Node * node, IDnum firstStrain)$/;"	f
getAbsolutePassMarkerSeqID	passageMarker.c	/^IDnum getAbsolutePassMarkerSeqID(PassageMarkerI marker)$/;"	f
getAnchors	correctedGraph.c	/^static PassageMarkerList *getAnchors(PassageMarkerI marker, Node * nodeA,$/;"	f	file:
getAnnotSequenceID	roadMap.c	/^IDnum getAnnotSequenceID(Annotation * annot)$/;"	f
getAnnotationCount	roadMap.c	/^IDnum getAnnotationCount(RoadMap * rdmap)$/;"	f
getAnnotationLength	roadMap.c	/^Coordinate getAnnotationLength(Annotation * annot)$/;"	f
getArc	graph.c	/^Arc *getArc(Node * node)$/;"	f
getArcBetweenNodes	graph.c	/^Arc *getArcBetweenNodes(Node * originNode, Node * destinationNode,$/;"	f
getConnection	scaffold.c	/^Connection * getConnection(Node * node) {$/;"	f
getConnectionDestination	scaffold.c	/^Node * getConnectionDestination(Connection * connect) {$/;"	f
getConnectionDirectCount	scaffold.c	/^IDnum getConnectionDirectCount(Connection * connect) {$/;"	f
getConnectionDistance	scaffold.c	/^Coordinate getConnectionDistance(Connection * connect) {$/;"	f
getConnectionPairedCount	scaffold.c	/^IDnum getConnectionPairedCount(Connection * connect) {$/;"	f
getConnectionVariance	scaffold.c	/^double getConnectionVariance(Connection * connect) {$/;"	f
getDFibHeapSize	dfibHeap.c	/^IDnum getDFibHeapSize(DFibHeap * heap)$/;"	f
getDestination	graph.c	/^Node *getDestination(Arc * arc)$/;"	f
getDestination_pg	preGraph.c	/^IDnum getDestination_pg(PreArcI preArc, IDnum preNodeID)$/;"	f
getFinish	roadMap.c	/^Coordinate getFinish(Annotation * annot)$/;"	f
getFinishID	roadMap.c	/^IDnum getFinishID(Annotation * annot)$/;"	f
getFinishOffset	passageMarker.c	/^Coordinate getFinishOffset(PassageMarkerI marker)$/;"	f
getGap	graph.c	/^GapMarker *getGap(Node * node, Graph * graph)$/;"	f
getGapFinish	graph.c	/^Coordinate getGapFinish(GapMarker * marker)$/;"	f
getGapStart	graph.c	/^Coordinate getGapStart(GapMarker * marker)$/;"	f
getInsertLength	graph.c	/^Coordinate getInsertLength(Graph * graph, Category cat)$/;"	f
getInsertLength_var	graph.c	/^double getInsertLength_var(Graph * graph, Category cat)$/;"	f
getInsertionMarkerPosition	preGraphConstruction.c	/^Coordinate getInsertionMarkerPosition(InsertionMarker * marker)$/;"	f
getInverseNucleotideChar	tightString.c	/^char getInverseNucleotideChar(Coordinate nucleotideIndex,$/;"	f
getKey	dfibHeap.c	/^Time getKey(DFibHeapNode * node)$/;"	f
getKmerKey	kmer.c	/^KmerKey getKmerKey(Kmer * kmer) {$/;"	f
getKmerOccurenceNodeID	kmerOccurenceTable.c	/^IDnum getKmerOccurenceNodeID(KmerOccurence * occurence) {$/;"	f
getKmerOccurencePosition	kmerOccurenceTable.c	/^Coordinate getKmerOccurencePosition(KmerOccurence * occurence) {$/;"	f
getLength	tightString.c	/^IDnum getLength(TightString * tString)$/;"	f
getMarkedNodeList	shortReadPairs.c	/^NodeList *getMarkedNodeList()$/;"	f
getMarker	graph.c	/^PassageMarkerI getMarker(Node * node)$/;"	f
getMostAppropriateHit	splayTable.c	/^static KmerOccurence * getMostAppropriateHit(Coordinate readCoord, Coordinate readLength, boolean direct, KmerOccurence * kmerOccurence, IDnum mapCount, IDnum * mapSequenceID, Coordinate * mapCoord, int wordLength) {$/;"	f	file:
getMultiplicity	graph.c	/^IDnum getMultiplicity(Arc * arc)$/;"	f
getMultiplicity_pg	preGraph.c	/^IDnum getMultiplicity_pg(PreArcI preArc)$/;"	f
getNearestHSPIndex	splayTable.c	/^static Coordinate getNearestHSPIndex(Coordinate position, IDnum * sequenceIDs, Coordinate sequenceLength) {$/;"	f	file:
getNextAnnotation	roadMap.c	/^Annotation *getNextAnnotation(Annotation * annot)$/;"	f
getNextArc	graph.c	/^Arc *getNextArc(Arc * arc)$/;"	f
getNextConnection	scaffold.c	/^Connection * getNextConnection(Connection * connect) {$/;"	f
getNextGap	graph.c	/^GapMarker *getNextGap(GapMarker * marker)$/;"	f
getNextInNode	passageMarker.c	/^PassageMarkerI getNextInNode(PassageMarkerI marker)$/;"	f
getNextInSequence	passageMarker.c	/^PassageMarkerI getNextInSequence(PassageMarkerI marker)$/;"	f
getNextKmerOccurence	kmerOccurenceTable.c	/^KmerOccurence * getNextKmerOccurence(KmerOccurence * current) {$/;"	f
getNextPreArc_pg	preGraph.c	/^PreArcI getNextPreArc_pg(PreArcI preArc, IDnum preNodeID)$/;"	f
getNode	passageMarker.c	/^Node *getNode(PassageMarkerI marker)$/;"	f
getNodeDHeapNode	correctedGraph.c	/^static DFibHeapNode *getNodeDHeapNode(Node * node)$/;"	f	file:
getNodeID	graph.c	/^IDnum getNodeID(Node * node)$/;"	f
getNodeInGraph	graph.c	/^Node *getNodeInGraph(Graph * graph, IDnum nodeID)$/;"	f
getNodeLength	graph.c	/^Coordinate getNodeLength(Node * node)$/;"	f
getNodePrevious	correctedGraph.c	/^static Node *getNodePrevious(Node * node)$/;"	f	file:
getNodePrevious	locallyCorrectedGraph.c	/^static Node *getNodePrevious(Node * node)$/;"	f	file:
getNodeReadCount	graph.c	/^IDnum getNodeReadCount(Node * node, Graph * graph)$/;"	f
getNodeReadCounts	graph.c	/^IDnum *getNodeReadCounts(Graph * graph)$/;"	f
getNodeReads	graph.c	/^ShortReadMarker *getNodeReads(Node * node, Graph * graph)$/;"	f
getNodeStatus	graph.c	/^boolean getNodeStatus(Node * node)$/;"	f
getNodeTime	correctedGraph.c	/^static Time getNodeTime(Node * node)$/;"	f	file:
getNodeTime	locallyCorrectedGraph.c	/^static Time getNodeTime(Node * node)$/;"	f	file:
getNodeToReadMappings	graph.c	/^ShortReadMarker **getNodeToReadMappings(Graph * graph)$/;"	f
getNucleotide	tightString.c	/^Nucleotide getNucleotide(Coordinate nucleotideIndex, TightString * tString)$/;"	f
getNucleotideChar	tightString.c	/^char getNucleotideChar(Coordinate nucleotideIndex, TightString * tString)$/;"	f
getNucleotideFromString	tightString.c	/^Nucleotide getNucleotideFromString(Coordinate nucleotideIndex,$/;"	f
getNucleotideInDescriptor	graph.c	/^static Nucleotide getNucleotideInDescriptor(Descriptor * descriptor,$/;"	f	file:
getNucleotideInDescriptor_pg	preGraph.c	/^static Nucleotide getNucleotideInDescriptor_pg(Descriptor * descriptor,$/;"	f	file:
getNucleotideInNode	graph.c	/^Nucleotide getNucleotideInNode(Node * node, Coordinate index) {$/;"	f
getOrigin	graph.c	/^Node *getOrigin(Arc * arc)$/;"	f
getOriginalVirtualCoverage	graph.c	/^Coordinate getOriginalVirtualCoverage(Node * node, Category category)$/;"	f
getOtherEnd_pg	preGraph.c	/^IDnum getOtherEnd_pg(PreArcI preArc, IDnum preNodeID)$/;"	f
getPassageMarkerFinish	passageMarker.c	/^Coordinate getPassageMarkerFinish(PassageMarkerI marker)$/;"	f
getPassageMarkerLength	passageMarker.c	/^Coordinate getPassageMarkerLength(PassageMarkerI marker)$/;"	f
getPassageMarkerSequenceID	passageMarker.c	/^IDnum getPassageMarkerSequenceID(PassageMarkerI marker)$/;"	f
getPassageMarkerStart	passageMarker.c	/^Coordinate getPassageMarkerStart(PassageMarkerI marker)$/;"	f
getPassageMarkerStatus	passageMarker.c	/^boolean getPassageMarkerStatus(PassageMarkerI marker)$/;"	f
getPosition	roadMap.c	/^Coordinate getPosition(Annotation * annot)$/;"	f
getPreArcBetweenPreNodes_pg	preGraph.c	/^PreArcI getPreArcBetweenPreNodes_pg(IDnum originPreNodeID,$/;"	f
getPreArc_pg	preGraph.c	/^PreArcI getPreArc_pg(IDnum preNodeID, PreGraph * preGraph)$/;"	f
getPreNodeInPreGraph_pg	preGraph.c	/^PreNode *getPreNodeInPreGraph_pg(PreGraph * preGraph, IDnum preNodeID)$/;"	f
getPreNodeLength_pg	preGraph.c	/^Coordinate getPreNodeLength_pg(IDnum preNodeID, PreGraph * preGraph)$/;"	f
getPreviousInSequence	passageMarker.c	/^PassageMarkerI getPreviousInSequence(PassageMarkerI marker)$/;"	f
getReadLength	graphStats.c	/^static Coordinate getReadLength(PassageMarkerI marker)$/;"	f	file:
getRecycleBinInArray	recycleBin.c	/^RecycleBin *getRecycleBinInArray(RecycleBin *recycleBin,$/;"	f
getReferenceCount	graphStats.c	/^static IDnum getReferenceCount(ReadSet * reads) {$/;"	f	file:
getRoadMapInArray	roadMap.c	/^RoadMap *getRoadMapInArray(RoadMapArray * array, IDnum index)$/;"	f
getSequenceLengths	readSet.c	/^IDnum *getSequenceLengths(ReadSet * reads, int wordLength)$/;"	f
getSequenceLengthsFromFile	readSet.c	/^IDnum *getSequenceLengthsFromFile(char *filename, int wordLength) \/* SF TODO This could also be chopped down to IDnum *\/$/;"	f
getShortReadMarkerAtIndex	graph.c	/^ShortReadMarker *getShortReadMarkerAtIndex(ShortReadMarker * array,$/;"	f
getShortReadMarkerID	graph.c	/^IDnum getShortReadMarkerID(ShortReadMarker * marker)$/;"	f
getShortReadMarkerOffset	graph.c	/^inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker)$/;"	f
getShortReadMarkerPosition	graph.c	/^inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker)$/;"	f
getStart	roadMap.c	/^Coordinate getStart(Annotation * annot)$/;"	f
getStartID	roadMap.c	/^IDnum getStartID(Annotation * annot)$/;"	f
getStartOffset	passageMarker.c	/^Coordinate getStartOffset(PassageMarkerI marker)$/;"	f
getTightStringInArray	tightString.c	/^TightString *getTightStringInArray(TightString * tString,$/;"	f
getTipLength	correctedGraph.c	/^static Coordinate getTipLength(Node * node)$/;"	f	file:
getTotalCoverage	graphStats.c	/^static Coordinate getTotalCoverage(Node * node)$/;"	f	file:
getTwinConnection	scaffold.c	/^Connection * getTwinConnection(Connection * connect) {$/;"	f
getTwinMarker	passageMarker.c	/^PassageMarkerI getTwinMarker(PassageMarkerI marker)$/;"	f
getTwinNode	graph.c	/^Node *getTwinNode(Node * node)$/;"	f
getUniqueness	graph.c	/^boolean getUniqueness(Node * node)$/;"	f
getVirtualCoverage	graph.c	/^Coordinate getVirtualCoverage(Node * node, Category category)$/;"	f
getWordLength	graph.c	/^int getWordLength(Graph * graph)$/;"	f
getWordLength_pg	preGraph.c	/^int getWordLength_pg(PreGraph * preGraph)$/;"	f
ghostThreadSequenceThroughGraph	graphReConstruction.c	/^static void ghostThreadSequenceThroughGraph(TightString * tString,$/;"	f	file:
goToEndOfLine	readSet.c	/^void goToEndOfLine(char *line, FILE * file)$/;"	f
goesToNode	readCoherentGraph.c	/^static boolean goesToNode(PassageMarkerI marker, Node * node)$/;"	f	file:
goesToNode	shortReadPairs.c	/^static boolean goesToNode(PassageMarkerI marker, Node * node)$/;"	f	file:
graph	correctedGraph.c	/^static Graph *graph;$/;"	v	file:
graph	locallyCorrectedGraph.c	/^static Graph *graph;$/;"	v	file:
graph	readCoherentGraph.c	/^static Graph *graph = NULL;$/;"	v	file:
graph	scaffold.c	/^static Graph *graph;$/;"	v	file:
graph	shortReadPairs.c	/^static Graph *graph;$/;"	v	file:
graph_st	graph.c	/^struct graph_st {$/;"	s	file:
grossErrorRemoval	graphStats.c	/^void grossErrorRemoval(Graph * graph, IDnum firstStrain)$/;"	f
handicapNode	shortReadPairs.c	/^void handicapNode(Node * node)$/;"	f
hasReferenceMarker	graphStats.c	/^static boolean hasReferenceMarker(Node * node, ReadSet * reads) {$/;"	f	file:
hasSingleArc	graph.c	/^boolean hasSingleArc(Node * node)$/;"	f
hasSinglePreArc_pg	preGraph.c	/^boolean hasSinglePreArc_pg(IDnum preNodeID, PreGraph * preGraph)$/;"	f
hash_kmer	splayTable.c	/^static KmerKey hash_kmer(Kmer * kmer)$/;"	f	file:
id_a	correctedGraph.c	/^	IDnum id_a;$/;"	m	struct:tkt_st	file:
id_b	correctedGraph.c	/^	IDnum id_b;$/;"	m	struct:tkt_st	file:
identifyUniqueNodes	readCoherentGraph.c	/^static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))$/;"	f	file:
idx	allocArray.c	/^	ArrayIdx idx;$/;"	m	struct:AllocArrayFreeElement_st	file:
importAnnotations	roadMap.c	/^Annotation *importAnnotations(FILE *file, IDnum * readIndex, IDnum * annotationCount)$/;"	f
importGraph	graph.c	/^Graph *importGraph(char *filename)$/;"	f
importPreGraph	graphReConstruction.c	/^Graph *importPreGraph(char *preGraphFilename, ReadSet * reads, char * roadmapFilename, $/;"	f
importReadSet	readSet.c	/^ReadSet *importReadSet(char *filename)$/;"	f
importRoadMapArray	roadMap.c	/^RoadMapArray *importRoadMapArray(char *filename)$/;"	f
importSimplifiedGraph	graph.c	/^Graph *importSimplifiedGraph(char *filename)$/;"	f
incrementAnnotationCoordinates	roadMap.c	/^void incrementAnnotationCoordinates(Annotation * annot)$/;"	f
incrementConnectionDistance	scaffold.c	/^void incrementConnectionDistance(Connection * connect, Coordinate increment) {$/;"	f
incrementFinishOffset	passageMarker.c	/^void incrementFinishOffset(PassageMarkerI marker, Coordinate offset)$/;"	f
incrementNodeReferenceMarkerCount_pg	preGraph.c	/^void incrementNodeReferenceMarkerCount_pg(PreGraph * preGraph, IDnum preNodeID) {$/;"	f
incrementOriginalVirtualCoverage	graph.c	/^void incrementOriginalVirtualCoverage(Node * node, Category category,$/;"	f
incrementReadStartCount	graph.c	/^void incrementReadStartCount(Node * node, Graph * graph)$/;"	f
incrementStartOffset	passageMarker.c	/^void incrementStartOffset(PassageMarkerI marker, Coordinate offset)$/;"	f
incrementVirtualCoverage	graph.c	/^void incrementVirtualCoverage(Node * node, Category category,$/;"	f
initRecycleBin	recycleBin.c	/^static void initRecycleBin(RecycleBin *recycleBin,$/;"	f	file:
initSplayTreeMemory	splay.c	/^void initSplayTreeMemory(void)$/;"	f
initializeReferenceMapping	graphStats.c	/^static void initializeReferenceMapping(ReferenceMapping * refMap, PassageMarkerI marker, Node * node) {$/;"	f	file:
initializeTodoLists	correctedGraph.c	/^static void initializeTodoLists()$/;"	f	file:
injectShortReads	graph.c	/^void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,$/;"	f
inputReferenceIntoSplayTable	splayTable.c	/^void inputReferenceIntoSplayTable(TightString * tString,$/;"	f	file:
inputSequenceArrayIntoSplayTableAndArchive	splayTable.c	/^void inputSequenceArrayIntoSplayTableAndArchive(ReadSet * reads,$/;"	f
inputSequenceIntoSplayTable	splayTable.c	/^void inputSequenceIntoSplayTable(TightString * array,$/;"	f
insertIntoTree	splay.c	/^void insertIntoTree(Kmer * kmer, SplayTree ** T)$/;"	f
insertLengths	graph.c	/^	Coordinate insertLengths[CATEGORIES + 1];$/;"	m	struct:graph_st	file:
insertLengths_var	graph.c	/^	double insertLengths_var[CATEGORIES + 1];$/;"	m	struct:graph_st	file:
insertNodeIntoDHeap	dfibHeap.c	/^DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key,$/;"	f
insertNodeIntoHeap	fibHeap.c	/^FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,$/;"	f
insertPassageMarker	graph.c	/^void insertPassageMarker(PassageMarkerI marker, Node * destination)$/;"	f
insertionMarker_st	preGraphConstruction.c	/^struct insertionMarker_st {$/;"	s	file:
int32	readSet.c	/^static int int32(const unsigned char * ptr)$/;"	f	file:
intLeftFilter	kmer.c	/^static const uint16_t intLeftFilter = (uint16_t) 3 << 14; $/;"	v	file:
intWordFilter	kmer.c	/^static uint16_t intWordFilter = (uint16_t) ((int16_t) -1); $/;"	v	file:
integrateDerivativeDistances	shortReadPairs.c	/^static void integrateDerivativeDistances(Connection * connect,$/;"	f	file:
isConnectedRead	graphStats.c	/^static boolean isConnectedRead(PassageMarkerI marker)$/;"	f	file:
isDestinationToMarker	passageMarker.c	/^boolean isDestinationToMarker(PassageMarkerI marker, Node * node)$/;"	f
isEligibleTip	concatenatedPreGraph.c	/^static boolean isEligibleTip(IDnum index, PreGraph * preGraph, Coordinate$/;"	f	file:
isError	graphStats.c	/^boolean isError(Node * node, IDnum firstStrain)$/;"	f
isInitial	passageMarker.c	/^boolean isInitial(PassageMarkerI marker)$/;"	f
isLocalDeadEnd	locallyCorrectedGraph.c	/^static boolean isLocalDeadEnd(Node * node)$/;"	f	file:
isLocalTwinDeadEnd	locallyCorrectedGraph.c	/^static boolean isLocalTwinDeadEnd(Node * node)$/;"	f	file:
isLoop_pg	preGraph.c	/^boolean isLoop_pg(PreArcI preArc)$/;"	f
isMinorityChoice	correctedGraph.c	/^static boolean isMinorityChoice(Node * node)$/;"	f	file:
isMixed	graphStats.c	/^boolean isMixed(Node * node, IDnum firstStrain)$/;"	f
isNatural	graphStats.c	/^boolean isNatural(Graph * graph)$/;"	f
isOnlyGenome	graphStats.c	/^boolean isOnlyGenome(Node * node, IDnum firstStrain)$/;"	f
isOnlyStrain	graphStats.c	/^boolean isOnlyStrain(Node * node, IDnum firstStrain)$/;"	f
isPreviousToNode	correctedGraph.c	/^static boolean isPreviousToNode(Node * previous, Node * target)$/;"	f	file:
isPreviousToNode	locallyCorrectedGraph.c	/^static boolean isPreviousToNode(Node * previous, Node * target)$/;"	f	file:
isSNP	graphStats.c	/^boolean isSNP(Node * node, IDnum firstStrain, int WORDLENGTH)$/;"	f
isSecondInPair	readSet.c	/^boolean isSecondInPair(ReadSet * reads, IDnum index)$/;"	f
isStart	preGraphConstruction.c	/^	boolean isStart;$/;"	m	struct:insertionMarker_st	file:
isTerminal	passageMarker.c	/^boolean isTerminal(PassageMarkerI marker)$/;"	f
isUniqueBasic	readCoherentGraph.c	/^boolean isUniqueBasic(Node * node)$/;"	f
isUniqueSolexa	readCoherentGraph.c	/^boolean isUniqueSolexa(Node * node)$/;"	f
keyFilter	kmer.c	/^static uint64_t keyFilter = 0;$/;"	v	file:
keyFilterIndex	kmer.c	/^static int keyFilterIndex = UNDEFINED;$/;"	v	file:
keyFilterLength	kmer.c	/^static int keyFilterLength = 0;$/;"	v	file:
keyFilterOffset	kmer.c	/^static int keyFilterOffset = 0;$/;"	v	file:
keyInAccelerationTable	kmerOccurenceTable.c	/^static inline KmerKey keyInAccelerationTable(Kmer * kmer,$/;"	f	file:
kmer	kmerOccurenceTable.c	/^	Kmer kmer;$/;"	m	struct:kmerOccurence_st	file:
kmer	splay.c	/^	Kmer kmer;$/;"	m	struct:splayNode_st	file:
kmerFilterIndex	kmer.c	/^static int kmerFilterIndex = UNDEFINED;$/;"	v	file:
kmerFilterLength	kmer.c	/^static int kmerFilterLength = 0;$/;"	v	file:
kmerFilterOffset	kmer.c	/^static int kmerFilterOffset = 0;$/;"	v	file:
kmerOccurenceIndex	kmerOccurenceTable.c	/^	IDnum kmerOccurenceIndex;$/;"	m	struct:kmerOccurenceTable_st	file:
kmerOccurencePtr	kmerOccurenceTable.c	/^	KmerOccurence * kmerOccurencePtr;$/;"	m	struct:kmerOccurenceTable_st	file:
kmerOccurenceTable	splayTable.c	/^	KmerOccurenceTable *kmerOccurenceTable;$/;"	m	struct:splayTable_st	file:
kmerOccurenceTable_st	kmerOccurenceTable.c	/^struct kmerOccurenceTable_st {$/;"	s	file:
kmerOccurence_st	kmerOccurenceTable.c	/^struct kmerOccurence_st {$/;"	s	file:
kmerTable	kmerOccurenceTable.c	/^	KmerOccurence *kmerTable;$/;"	m	struct:kmerOccurenceTable_st	file:
kmerTableSize	kmerOccurenceTable.c	/^	IDnum kmerTableSize;$/;"	m	struct:kmerOccurenceTable_st	file:
left	splay.c	/^	struct splayNode_st *left;$/;"	m	struct:splayNode_st	typeref:struct:splayNode_st::splayNode_st	file:
length	graph.c	/^	IDnum length;	\/\/ 32$/;"	m	struct:node_st	file:
length	graph.c	/^	IDnum length;$/;"	m	struct:gapMarker_st	file:
length	graphReConstruction.c	/^	IDnum length;$/;"	m	struct:referenceMapping_st	file:
length	preGraph.c	/^	IDnum length;$/;"	m	struct:preMarker_st	file:
length	preGraph.c	/^	IDnum length;$/;"	m	struct:preNode_st	file:
length	roadMap.c	/^	ShortLength length;	\/\/ 32$/;"	m	struct:annotation_st	file:
length	tightString.c	/^	IDnum length;$/;"	m	struct:tString_st	file:
listMemory	passageMarker.c	/^static RecycleBin *listMemory = NULL;$/;"	v	file:
listMemory	readCoherentGraph.c	/^static RecycleBin *listMemory = NULL;$/;"	v	file:
localScaffold	shortReadPairs.c	/^static MiniConnection *localScaffold = NULL;$/;"	v	file:
lockNode	graphReConstruction.c	/^static inline void lockNode(Node *node)$/;"	f	file:
locks	concatenatedPreGraph.c	/^static volatile boolean * locks = NULL;$/;"	v	file:
logFinalStats	graphStats.c	/^void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *directory)$/;"	f
logInstructions	readSet.c	/^void logInstructions(int argc, char **argv, char *directory)$/;"	f
longLeftFilter	kmer.c	/^static const uint32_t longLeftFilter = (uint32_t) 3 << 30; $/;"	v	file:
longLongKeyFilterIndex	kmer.c	/^static int longLongKeyFilterIndex = KMER_LONGLONGS - 1;$/;"	v	file:
longLongKmerFilter	kmer.c	/^static uint64_t longLongKmerFilter = (uint64_t) ((int64_t) -1); $/;"	v	file:
longLongKmerFilterIndex	kmer.c	/^static int longLongKmerFilterIndex = KMER_LONGLONGS - 1;$/;"	v	file:
longLongLeftFilter	kmer.c	/^static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; $/;"	v	file:
longLongWordFilter	kmer.c	/^static uint64_t longLongWordFilter = (uint64_t) ((int64_t) -1); $/;"	v	file:
longWordFilter	kmer.c	/^static uint32_t longWordFilter = (uint32_t) ((int32_t) -1); $/;"	v	file:
main	run.c	/^int main(int argc, char **argv)$/;"	f
main	run2.c	/^int main(int argc, char **argv)$/;"	f
mallocOrExit3	utility.c	/^void *mallocOrExit3(size_t count, size_t size, const char *name)$/;"	f
mapDistancesOntoPaths	correctedGraph.c	/^static Coordinate mapDistancesOntoPaths()$/;"	f	file:
mapSlowOntoFast	correctedGraph.c	/^static void mapSlowOntoFast()$/;"	f	file:
markInterestingNodes	shortReadPairs.c	/^static void markInterestingNodes(Node * node)$/;"	f	file:
markedNodes	shortReadPairs.c	/^static NodeList *markedNodes;$/;"	v	file:
marker	graph.c	/^	PassageMarkerI marker;	\/\/ 32$/;"	m	struct:node_st	file:
marker	readCoherentGraph.c	/^	PassageMarkerI marker;$/;"	m	struct:rb_connection_st	file:
markerCount	graph.c	/^IDnum markerCount(Node * node)$/;"	f
markerFollowsPath	correctedGraph.c	/^static boolean markerFollowsPath(PassageMarkerI marker,$/;"	f	file:
markerLeadsToArc	correctedGraph.c	/^static boolean markerLeadsToArc(PassageMarkerI marker, Node * nodeA,$/;"	f	file:
markerLeadsToNode	correctedGraph.c	/^static boolean markerLeadsToNode(PassageMarkerI marker, Node * node)$/;"	f	file:
markerMemory	passageMarker.c	/^static AllocArray *markerMemory = NULL;$/;"	v	file:
max	correctedGraph.c	/^static Time max(Time A, Time B, Time C)$/;"	f	file:
max	locallyCorrectedGraph.c	/^static Time max(Time A, Time B, Time C)$/;"	f	file:
maxLength	graphStats.c	/^Coordinate maxLength(Graph * graph)$/;"	f
measureCoOccurences	scaffold.c	/^static void measureCoOccurences(Coordinate ** coOccurences, boolean * interestingReads, ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {$/;"	f	file:
measureTangleSizes	graphStats.c	/^void measureTangleSizes(Graph * graph, Coordinate maxLength)$/;"	f
memorizeNode	graphReConstruction.c	/^static void memorizeNode(Node * node, SmallNodeList ** nodePile)$/;"	f	file:
mergeArcLists	graph.c	/^static Arc *mergeArcLists(Arc * left, Arc * right)$/;"	f	file:
mergeDescriptors	graph.c	/^static inline Descriptor *mergeDescriptors(Descriptor * descr,$/;"	f	file:
mergeDescriptorsF2F_pg	preGraph.c	/^static inline Descriptor *mergeDescriptorsF2F_pg(Descriptor * descr,$/;"	f	file:
mergeDescriptorsH2H_pg	preGraph.c	/^static inline Descriptor *mergeDescriptorsH2H_pg(Descriptor * descr,$/;"	f	file:
mergeDescriptors_pg	preGraph.c	/^static inline Descriptor *mergeDescriptors_pg(Descriptor * descr,$/;"	f	file:
mergeGapMarkerLists	graph.c	/^static GapMarker *mergeGapMarkerLists(GapMarker * left, GapMarker * right)$/;"	f	file:
mergeNodeReads	graph.c	/^void mergeNodeReads(Node * target, Node * source, Graph * graph)$/;"	f
min	graph.c	/^static inline Coordinate min(Coordinate A, Coordinate B)$/;"	f	file:
minKeyOfHeap	fibHeap.c	/^Coordinate minKeyOfHeap(FibHeap * heap)$/;"	f
min_short	graph.c	/^static inline ShortLength min_short(ShortLength A, ShortLength B)$/;"	f	file:
miniConnection_st	shortReadPairs.c	/^struct miniConnection_st {$/;"	s	file:
multCounter	readCoherentGraph.c	/^static IDnum multCounter = 0;$/;"	v	file:
multiplicity	graph.c	/^	IDnum multiplicity;	\/\/ 32$/;"	m	struct:arc_st	file:
multiplicity	preGraph.c	/^	IDnum multiplicity;$/;"	m	struct:preArc_st	file:
multiplicity	readCoherentGraph.c	/^	IDnum multiplicity;$/;"	m	struct:rb_connection_st	file:
n50	graphStats.c	/^Coordinate n50(Graph * graph)$/;"	f
name	graphStats.c	/^	char * name;$/;"	m	struct:referenceCoord_st	file:
name	readSet.c	/^	char * name;$/;"	m	struct:referenceCoordinate_st	file:
newAllocArray	allocArray.c	/^newAllocArray (size_t elementSize, char *name)$/;"	f
newDFibHeap	dfibHeap.c	/^DFibHeap *newDFibHeap()$/;"	f
newDescriptor	graph.c	/^static Descriptor *newDescriptor(IDnum sequenceID, Coordinate start,$/;"	f	file:
newDescriptor_pg	preGraph.c	/^static Descriptor *newDescriptor_pg(Coordinate length, FILE * file,$/;"	f	file:
newFibHeap	fibHeap.c	/^FibHeap *newFibHeap()$/;"	f
newKmerOccurenceTable	kmerOccurenceTable.c	/^KmerOccurenceTable * newKmerOccurenceTable(short int accelerationBits, int wordLength) {$/;"	f
newNegativeDescriptor	graph.c	/^static Descriptor *newNegativeDescriptor(IDnum sequenceID,$/;"	f	file:
newNode	graph.c	/^Node *newNode(IDnum sequenceID, Coordinate start, Coordinate finish,$/;"	f
newPassageMarker	passageMarker.c	/^PassageMarkerI newPassageMarker(IDnum seqID, Coordinate start,$/;"	f
newPassageMarkerList	passageMarker.c	/^PassageMarkerList *newPassageMarkerList(PassageMarkerI marker,$/;"	f
newPositiveDescriptor	graph.c	/^static Descriptor *newPositiveDescriptor(IDnum sequenceID,$/;"	f	file:
newPreGraph_pg	preGraphConstruction.c	/^PreGraph *newPreGraph_pg(RoadMapArray * rdmapArray, char *sequenceFilename)$/;"	f
newQueueTicket	correctedGraph.c	/^static void newQueueTicket(IDnum id_a, IDnum id_b)$/;"	f	file:
newReadCoverage	graphStats.c	/^Coordinate newReadCoverage(Node * node, IDnum firstStrain)$/;"	f
newReadSet	readSet.c	/^ReadSet *newReadSet()$/;"	f
newReadSetAroundTightStringArray	readSet.c	/^ReadSet *newReadSetAroundTightStringArray(TightString ** array,$/;"	f
newRecycleBin	recycleBin.c	/^RecycleBin *newRecycleBin(size_t node_size, int nodes_per_chunk)$/;"	f
newRecycleBinArray	recycleBin.c	/^RecycleBin *newRecycleBinArray(unsigned int n,$/;"	f
newReferenceCoordinateTable	readSet.c	/^static ReferenceCoordinateTable * newReferenceCoordinateTable() {$/;"	f	file:
newRoadMap	roadMap.c	/^RoadMap *newRoadMap()$/;"	f
newSplayTable	splayTable.c	/^SplayTable *newSplayTable(int WORDLENGTH, boolean double_strand)$/;"	f
newSplayTree	splay.c	/^SplayTree *newSplayTree()$/;"	f
newTicket	correctedGraph.c	/^static Ticket *newTicket()$/;"	f	file:
newTightString	tightString.c	/^TightString *newTightString(Coordinate length)$/;"	f
newTightStringArrayFromStringArray	tightString.c	/^TightString *newTightStringArrayFromStringArray(char **sequences,$/;"	f
newTightStringFromString	tightString.c	/^TightString *newTightStringFromString(char *sequence)$/;"	f
next	allocArray.c	/^	AllocArrayFreeElement *next;$/;"	m	struct:AllocArrayFreeElement_st	file:
next	correctedGraph.c	/^	Ticket *next;$/;"	m	struct:tkt_st	file:
next	graph.c	/^	Arc *next;		\/\/ 64$/;"	m	struct:arc_st	file:
next	graph.c	/^	GapMarker *next;$/;"	m	struct:gapMarker_st	file:
next	graphReConstruction.c	/^	SmallNodeList *next;$/;"	m	struct:smallNodeList_st	file:
next	preGraph.c	/^	PreMarker * next;$/;"	m	struct:preMarker_st	file:
next	readCoherentGraph.c	/^	RBConnection *next;$/;"	m	struct:rb_connection_st	file:
next	recycleBin.c	/^	struct RecycleBin_Node *next;$/;"	m	struct:RecycleBin_Node	typeref:struct:RecycleBin_Node::RecycleBin_Node	file:
next	recycleBin.c	/^	struct chunk_st *next;$/;"	m	struct:chunk_st	typeref:struct:chunk_st::chunk_st	file:
next	scaffold.c	/^	Connection *next;$/;"	m	struct:connection_st	file:
nextInLookupTable	graph.c	/^	Arc *nextInLookupTable;	\/\/ 64$/;"	m	struct:arc_st	file:
nextInNode	passageMarker.c	/^	PassageMarkerI nextInNode;$/;"	m	struct:passage_st	file:
nextInSequence	passageMarker.c	/^	PassageMarkerI nextInSequence;$/;"	m	struct:passage_st	file:
nextLeft	preGraph.c	/^	PreArcI nextLeft; \/* Index of the previous PreArc *\/$/;"	m	struct:preArc_st	file:
nextRight	preGraph.c	/^	PreArcI nextRight; \/* Index of the next PreArc *\/$/;"	m	struct:preArc_st	file:
nextStartingPoint	correctedGraph.c	/^static Node *nextStartingPoint()$/;"	f	file:
nextTodoTicket	correctedGraph.c	/^static IDnum nextTodoTicket()$/;"	f	file:
node	graphReConstruction.c	/^	Node *node;$/;"	m	struct:smallNodeList_st	file:
node	passageMarker.c	/^	struct node_st *node;$/;"	m	struct:passage_st	typeref:struct:passage_st::node_st	file:
node	readCoherentGraph.c	/^	Node *node;$/;"	m	struct:rb_connection_st	file:
nodeCount	graph.c	/^	IDnum nodeCount;$/;"	m	struct:graph_st	file:
nodeCount	graph.c	/^IDnum nodeCount(Graph * graph)$/;"	f
nodeGenomicMultiplicity	graphStats.c	/^int nodeGenomicMultiplicity(Node * node, IDnum firstStrain)$/;"	f
nodeID	graphReConstruction.c	/^	IDnum nodeID;$/;"	m	struct:nodeMask_st	file:
nodeID	graphReConstruction.c	/^	IDnum nodeID;$/;"	m	struct:referenceMapping_st	file:
nodeID	kmerOccurenceTable.c	/^	IDnum nodeID;$/;"	m	struct:kmerOccurence_st	file:
nodeID	roadMap.c	/^	IDnum nodeID;$/;"	m	union:positionPtr	file:
nodeID	scaffold.c	/^	IDnum nodeID;$/;"	m	struct:readOccurence_st	file:
nodeList	shortReadPairs.c	/^	NodeList *nodeList;$/;"	m	struct:miniConnection_st	file:
nodeListMemory	readCoherentGraph.c	/^static RecycleBin *nodeListMemory = NULL;$/;"	v	file:
nodeListMemory	shortReadPairs.c	/^static RecycleBin *nodeListMemory = NULL;$/;"	v	file:
nodeLocks	graphReConstruction.c	/^static omp_lock_t *nodeLocks = NULL;$/;"	v	file:
nodeMask_st	graphReConstruction.c	/^struct nodeMask_st {$/;"	s	file:
nodeMemorized	graphReConstruction.c	/^static boolean nodeMemorized(Node * node, SmallNodeList * nodePile) {$/;"	f	file:
nodeMemory	graph.c	/^static RecycleBin *nodeMemory = NULL;$/;"	v	file:
nodeMultiplicity	graphStats.c	/^IDnum nodeMultiplicity(Node * node)$/;"	f
nodeReadCounts	graph.c	/^	IDnum *nodeReadCounts;$/;"	m	struct:graph_st	file:
nodeReads	graph.c	/^	ShortReadMarker **nodeReads;$/;"	m	struct:graph_st	file:
nodeReferenceMarkerCounts	preGraph.c	/^	IDnum * nodeReferenceMarkerCounts;$/;"	m	struct:preGraph_st	file:
nodeReferenceMarkers	preGraph.c	/^	PreMarker ** nodeReferenceMarkers;$/;"	m	struct:preGraph_st	file:
nodeStart	graphReConstruction.c	/^	IDnum nodeStart;$/;"	m	struct:referenceMapping_st	file:
nodeStatistics	graphStats.c	/^char *nodeStatistics(Node * node)$/;"	f
node_size	recycleBin.c	/^	size_t node_size;$/;"	m	struct:recycleBin_st	file:
node_st	graph.c	/^struct node_st {$/;"	s	file:
nodes	graph.c	/^	Node **nodes;$/;"	m	struct:graph_st	file:
nodes_per_chunk	recycleBin.c	/^	int nodes_per_chunk;$/;"	m	struct:recycleBin_st	file:
norm	scaffold.c	/^static double norm(double X)$/;"	f	file:
normInt	scaffold.c	/^static double normInt(double X, double Y)$/;"	f	file:
nullCounter	readCoherentGraph.c	/^static IDnum nullCounter = 0;$/;"	v	file:
offset	graph.c	/^	ShortLength offset;$/;"	m	struct:shortReadMarker_st	file:
offset	scaffold.c	/^	IDnum offset;$/;"	m	struct:readOccurence_st	file:
orderInsertionMarkers	preGraphConstruction.c	/^orderInsertionMarkers(InsertionMarker ** insMarkers,$/;"	f	file:
orderNodeReadStartArrays	graph.c	/^void orderNodeReadStartArrays(Graph * graph)$/;"	f
originalVirtualCoverage	graph.c	/^	IDnum originalVirtualCoverage[CATEGORIES];	\/\/ 32 * 2$/;"	m	struct:node_st	file:
outDegree	graph.c	/^int outDegree(Node * node)$/;"	f
ownerThreads	graphReConstruction.c	/^static int *ownerThreads = NULL;$/;"	v	file:
pairedCategories	readSet.c	/^int pairedCategories(ReadSet * reads)$/;"	f
paired_count	scaffold.c	/^	IDnum paired_count;$/;"	m	struct:connection_st	file:
parseDataAndReadFiles	readSet.c	/^void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand)$/;"	f
passageMarkerDirection	passageMarker.c	/^int passageMarkerDirection(PassageMarkerI marker)$/;"	f
passage_st	passageMarker.c	/^struct passage_st {$/;"	s	file:
path	readCoherentGraph.c	/^static PassageMarkerI path = NULL_IDX;$/;"	v	file:
pathContainsReference	correctedGraph.c	/^static boolean pathContainsReference(PassageMarkerI path) {$/;"	f	file:
pathIsClear	shortReadPairs.c	/^static NodeList *pathIsClear(Node * node, Node * oppositeNode,$/;"	f	file:
placeOccurenceInSplayTree	splay.c	/^placeOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,$/;"	f
popNodeRecord	shortReadPairs.c	/^static Node *popNodeRecord()$/;"	f	file:
popNucleotide	kmer.c	/^Nucleotide popNucleotide(Kmer * kmer) {$/;"	f
position	graph.c	/^	IDnum position;$/;"	m	struct:gapMarker_st	file:
position	graph.c	/^	IDnum position;$/;"	m	struct:shortReadMarker_st	file:
position	kmerOccurenceTable.c	/^	IDnum position;$/;"	m	struct:kmerOccurence_st	file:
position	roadMap.c	/^	ShortLength position;	\/\/ 32$/;"	m	struct:annotation_st	file:
position	scaffold.c	/^	IDnum position;$/;"	m	struct:readOccurence_st	file:
position	splay.c	/^	Coordinate position;$/;"	m	struct:splayNode_st	file:
positionPtr	roadMap.c	/^union positionPtr {$/;"	u	file:
positive_strand	graphStats.c	/^	boolean positive_strand;$/;"	m	struct:referenceCoord_st	file:
positive_strand	readSet.c	/^	boolean positive_strand;$/;"	m	struct:referenceCoordinate_st	file:
preArcLeft	preGraph.c	/^	PreArcI preArcLeft;$/;"	m	struct:preNode_st	file:
preArcMemory	preGraph.c	/^static AllocArray *preArcMemory = NULL;$/;"	v	file:
preArcRight	preGraph.c	/^	PreArcI preArcRight;$/;"	m	struct:preNode_st	file:
preArc_st	preGraph.c	/^struct preArc_st {$/;"	s	file:
preGraph_st	preGraph.c	/^struct preGraph_st {$/;"	s	file:
preMarker_st	preGraph.c	/^struct preMarker_st {$/;"	s	file:
preNodeCount	preGraph.c	/^	IDnum preNodeCount;$/;"	m	struct:preGraph_st	file:
preNodeCount_pg	preGraph.c	/^IDnum preNodeCount_pg(PreGraph * preGraph)$/;"	f
preNodeID	preGraph.c	/^	IDnum preNodeID; \/* SF TODO only the sign seems to matter. Could replace with char or bit field *\/$/;"	m	struct:preMarker_st	file:
preNodeIDLeft	preGraph.c	/^	IDnum preNodeIDLeft;$/;"	m	struct:preArc_st	file:
preNodeIDRight	preGraph.c	/^	IDnum preNodeIDRight;$/;"	m	struct:preArc_st	file:
preNodeStart	preGraph.c	/^	IDnum preNodeStart;$/;"	m	struct:preMarker_st	file:
preNode_st	preGraph.c	/^struct preNode_st {$/;"	s	file:
preNodes	preGraph.c	/^	PreNode *preNodes;$/;"	m	struct:preGraph_st	file:
prepareGraphForLocalCorrections	locallyCorrectedGraph.c	/^void prepareGraphForLocalCorrections(Graph * argGraph)$/;"	f
previous	correctedGraph.c	/^static Node **previous;$/;"	v	file:
previous	graph.c	/^	Arc *previous;		\/\/ 64$/;"	m	struct:arc_st	file:
previous	locallyCorrectedGraph.c	/^static Node **previous;$/;"	v	file:
previous	preGraph.c	/^	PreMarker * previous;$/;"	m	struct:preMarker_st	file:
previous	scaffold.c	/^	Connection *previous;$/;"	m	struct:connection_st	file:
previousInNode	passageMarker.c	/^	PassageMarkerI previousInNode;$/;"	m	struct:passage_st	file:
printAnnotations	splayTable.c	/^static void printAnnotations(IDnum *sequenceIDs, Coordinate * coords,$/;"	f	file:
printConnections	scaffold.c	/^void printConnections(ReadSet * reads)$/;"	f
printKmer	kmer.c	/^void printKmer(Kmer * kmer) {$/;"	f
printShortCounts	graphStats.c	/^static void printShortCounts(FILE * outfile, Node * node, Graph * graph, ReadSet * reads) {$/;"	f	file:
printTree	splay.c	/^void printTree(SplayTree * T)$/;"	f
printUsage	readSet.c	/^static void printUsage()$/;"	f	file:
printUsage	run.c	/^static void printUsage()$/;"	f	file:
printUsage	run2.c	/^static void printUsage()$/;"	f	file:
programName	utility.c	/^static const char *programName = NULL;$/;"	v	file:
progressStatus	correctedGraph.c	/^static boolean *progressStatus;$/;"	v	file:
projectFromLongRead	scaffold.c	/^static void projectFromLongRead(Node * node, PassageMarkerI marker,$/;"	f	file:
projectFromNode	scaffold.c	/^static void projectFromNode(IDnum nodeID,$/;"	f	file:
projectFromReadPair	scaffold.c	/^static void projectFromReadPair(Node * node, ReadOccurence * readOccurence,$/;"	f	file:
projectFromShortRead	scaffold.c	/^static void projectFromShortRead(Node * node,$/;"	f	file:
projectFromSingleRead	scaffold.c	/^static void projectFromSingleRead(Node * node,$/;"	f	file:
projectGraphToFile	graphStats.c	/^void projectGraphToFile(Graph * graph, char *filename, int WORDLENGTH,$/;"	f
pushNeighbours	shortReadPairs.c	/^static boolean pushNeighbours(Node * node, Node * oppositeNode,$/;"	f	file:
pushNucleotide	kmer.c	/^void pushNucleotide(Kmer * kmer, Nucleotide nucleotide) {$/;"	f
rb_connection_st	readCoherentGraph.c	/^struct rb_connection_st {$/;"	s	file:
reConnectAnnotation	preGraphConstruction.c	/^static void reConnectAnnotation(IDnum * currentPreNodeID, Annotation * annot,$/;"	f	file:
readBAMFile	readSet.c	/^static void readBAMFile(FILE *outfile, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readBAMint32	readSet.c	/^static int readBAMint32(gzFile file)$/;"	f	file:
readCoherentGraph	readCoherentGraph.c	/^void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node),$/;"	f
readCoverage	graphStats.c	/^Coordinate readCoverage(Node * node)$/;"	f
readElandFile	readSet.c	/^static void readElandFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readFastAFile	readSet.c	/^static void readFastAFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readFastAGZFile	readSet.c	/^static void readFastAGZFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readFastQFile	readSet.c	/^static void readFastQFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readFastQGZFile	readSet.c	/^static void readFastQGZFile(FILE * outfile, char *filename, Category cat, IDnum *sequenceIndex)$/;"	f	file:
readID	graph.c	/^	IDnum readID;$/;"	m	struct:shortReadMarker_st	file:
readMAQGZFile	readSet.c	/^static void readMAQGZFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readNegativePassageMarker	sequenceExpander.c	/^static TightString *readNegativePassageMarker(PassageMarkerI marker,$/;"	f	file:
readNode	graph.c	/^char *readNode(Node * node)$/;"	f
readNucleotide	tightString.c	/^char readNucleotide(Nucleotide nucleotide)$/;"	f
readOccurence_st	scaffold.c	/^struct readOccurence_st {$/;"	s	file:
readPassageMarker	passageMarker.c	/^char *readPassageMarker(PassageMarkerI marker)$/;"	f
readPassageMarkerSequence	passageMarker.c	/^char *readPassageMarkerSequence(PassageMarkerI marker,$/;"	f
readPositivePassageMarker	sequenceExpander.c	/^static TightString *readPositivePassageMarker(PassageMarkerI marker,$/;"	f	file:
readPreGraphFile	graph.c	/^Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand)$/;"	f
readRawFile	readSet.c	/^static void readRawFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readRawGZFile	readSet.c	/^static void readRawGZFile(FILE * outfile, char *filename, Category cat, IDnum *sequenceIndex)$/;"	f	file:
readSAMFile	readSet.c	/^static void readSAMFile(FILE *outfile, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readSolexaFile	readSet.c	/^static void readSolexaFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readStarts	graphStats.c	/^IDnum readStarts(Node * node)$/;"	f
readStartsAreActivated	graph.c	/^boolean readStartsAreActivated(Graph * graph)$/;"	f
readTightString	tightString.c	/^char *readTightString(TightString * tString)$/;"	f
readTightStringFragment	tightString.c	/^void readTightStringFragment(TightString * tString, Coordinate start,$/;"	f
readjustConnection	scaffold.c	/^void readjustConnection(Connection * connect, Coordinate distance,$/;"	f
readjustMiniConnection	shortReadPairs.c	/^static void readjustMiniConnection(Node * node,$/;"	f	file:
reallocOrExit4	utility.c	/^void *reallocOrExit4(void *ptr, size_t count, size_t size, const char *name)$/;"	f
reallocOrExitReferenceMarkers	preGraph.c	/^static PreMarker * reallocOrExitReferenceMarkers(PreGraph * preGraph, IDnum preNodeID, IDnum length) {$/;"	f	file:
reallocateNodeDescriptor	graph.c	/^void reallocateNodeDescriptor(Node * node, Coordinate length) {$/;"	f
reassessArcMultiplicities	graph.c	/^void reassessArcMultiplicities(Graph * graph)$/;"	f
recenterLocalScaffold	shortReadPairs.c	/^static void recenterLocalScaffold(Node * node, Coordinate oldLength)$/;"	f	file:
recenterNode	shortReadPairs.c	/^static void recenterNode(Node * node, Coordinate oldLength)$/;"	f	file:
reconnectPassageMarker	shortReadPairs.c	/^static void reconnectPassageMarker(PassageMarkerI marker, Node * node,$/;"	f	file:
recordKmerOccurence	kmerOccurenceTable.c	/^void recordKmerOccurence(Kmer * kmer, IDnum nodeID, Coordinate position, KmerOccurenceTable * table) {$/;"	f
recordNode	shortReadPairs.c	/^static NodeList *recordNode(Node * node)$/;"	f	file:
recordReferenceMappings	graphReConstruction.c	/^static ReferenceMapping * recordReferenceMappings(char * preGraphFilename, IDnum arrayLength) {$/;"	f	file:
recycle	recycleBin.c	/^	RecycleBin_Node *recycle;$/;"	m	struct:recycleBin_st	file:
recycleBinAvailablePointers	recycleBin.c	/^size_t recycleBinAvailablePointers(RecycleBin * bin)$/;"	f
recycleBinFreeSpace	recycleBin.c	/^size_t recycleBinFreeSpace(RecycleBin * bin)$/;"	f
recycleBin_st	recycleBin.c	/^struct recycleBin_st {$/;"	s	file:
reduceNode	graph.c	/^void reduceNode(Node * node)$/;"	f
reduceSlowNodes	correctedGraph.c	/^static void reduceSlowNodes(PassageMarkerI slowMarker, Node * finish)$/;"	f	file:
refFinish	graphStats.c	/^	IDnum refFinish;$/;"	m	struct:refMap_st	file:
refID	graphStats.c	/^	IDnum refID;$/;"	m	struct:refMap_st	file:
refMap_st	graphStats.c	/^typedef struct refMap_st {$/;"	s	file:
refReadCoverage	graphStats.c	/^Coordinate refReadCoverage(Node * node, IDnum firstStrain)$/;"	f
refStart	graphStats.c	/^	IDnum refStart;$/;"	m	struct:refMap_st	file:
referenceCoord_st	graphStats.c	/^struct referenceCoord_st {$/;"	s	file:
referenceCoordinateTable_st	readSet.c	/^struct referenceCoordinateTable_st {$/;"	s	file:
referenceCoordinate_st	readSet.c	/^struct referenceCoordinate_st {$/;"	s	file:
referenceCount	preGraph.c	/^	IDnum referenceCount;$/;"	m	struct:preGraph_st	file:
referenceGraphKmers	graphReConstruction.c	/^static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,$/;"	f	file:
referenceID	graphReConstruction.c	/^	IDnum referenceID;$/;"	m	struct:referenceMapping_st	file:
referenceID	preGraph.c	/^	IDnum referenceID;$/;"	m	struct:preMarker_st	file:
referenceID	readSet.c	/^	IDnum referenceID;$/;"	m	struct:referenceCoordinate_st	file:
referenceMapping_st	graphReConstruction.c	/^struct referenceMapping_st {$/;"	s	file:
referenceMarkersAreActivated_pg	preGraph.c	/^boolean referenceMarkersAreActivated_pg(PreGraph * preGraph) {$/;"	f
referenceStart	graphReConstruction.c	/^	IDnum referenceStart;$/;"	m	struct:referenceMapping_st	file:
referenceStart	preGraph.c	/^	IDnum referenceStart;$/;"	m	struct:preMarker_st	file:
referenceStarts	preGraph.c	/^	PreMarker ** referenceStarts;$/;"	m	struct:preGraph_st	file:
reference_coordinate_double_strand	readSet.c	/^static Coordinate reference_coordinate_double_strand = true;$/;"	v	file:
remapBackOfNodeArcsOntoNeighbour	correctedGraph.c	/^static void remapBackOfNodeArcsOntoNeighbour(Node * source, Node * target)$/;"	f	file:
remapBackOfNodeDescriptorOntoNeighbour	correctedGraph.c	/^static void remapBackOfNodeDescriptorOntoNeighbour(Node * source,$/;"	f	file:
remapBackOfNodeMarkersOntoNeighbour	correctedGraph.c	/^remapBackOfNodeMarkersOntoNeighbour(Node * source,$/;"	f	file:
remapBackOfNodeOntoNeighbour	correctedGraph.c	/^remapBackOfNodeOntoNeighbour(Node * source, PassageMarkerI sourceMarker,$/;"	f	file:
remapBackOfNodeTimesOntoNeighbour	correctedGraph.c	/^static void remapBackOfNodeTimesOntoNeighbour(Node * source, Node * target)$/;"	f	file:
remapEmptyPathArcsOntoMiddlePathSimple	correctedGraph.c	/^static void remapEmptyPathArcsOntoMiddlePathSimple(PassageMarkerI emptyPath,$/;"	f	file:
remapEmptyPathMarkersOntoMiddlePathDevious	correctedGraph.c	/^static void remapEmptyPathMarkersOntoMiddlePathDevious(PassageMarkerI emptyPath,$/;"	f	file:
remapEmptyPathMarkersOntoMiddlePathSimple	correctedGraph.c	/^static void remapEmptyPathMarkersOntoMiddlePathSimple(PassageMarkerI emptyPath,$/;"	f	file:
remapEmptyPathOntoMiddlePath	correctedGraph.c	/^remapEmptyPathOntoMiddlePath(PassageMarkerI emptyPath,$/;"	f	file:
remapNodeArcsOntoNeighbour	correctedGraph.c	/^static void remapNodeArcsOntoNeighbour(Node * source, Node * target)$/;"	f	file:
remapNodeArcsOntoTarget	correctedGraph.c	/^static void remapNodeArcsOntoTarget(Node * source, Node * target)$/;"	f	file:
remapNodeFibHeapReferencesOntoNode	correctedGraph.c	/^remapNodeFibHeapReferencesOntoNode(Node * source, Node * target)$/;"	f	file:
remapNodeInwardReferencesOntoNode	correctedGraph.c	/^static void remapNodeInwardReferencesOntoNode(Node * source, Node * target)$/;"	f	file:
remapNodeMarkersOntoNeighbour	correctedGraph.c	/^static void remapNodeMarkersOntoNeighbour(Node * source,$/;"	f	file:
remapNodeOntoNeighbour	correctedGraph.c	/^static void remapNodeOntoNeighbour(Node * source,$/;"	f	file:
remapNodeTimesOntoForwardMiddlePath	correctedGraph.c	/^static void remapNodeTimesOntoForwardMiddlePath(Node * source,$/;"	f	file:
remapNodeTimesOntoNeighbour	correctedGraph.c	/^static void remapNodeTimesOntoNeighbour(Node * source, Node * target)$/;"	f	file:
remapNodeTimesOntoTargetNode	correctedGraph.c	/^static void remapNodeTimesOntoTargetNode(Node * source, Node * target)$/;"	f	file:
remapNodeTimesOntoTwinMiddlePath	correctedGraph.c	/^static void remapNodeTimesOntoTwinMiddlePath(Node * source,$/;"	f	file:
removeDead	graphStats.c	/^static boolean removeDead(PassageMarkerList ** list)$/;"	f	file:
removeHighCoverageNodes	graphStats.c	/^void removeHighCoverageNodes(Graph * graph, double maxCov)$/;"	f
removeLowCoverageNodes	graphStats.c	/^void removeLowCoverageNodes(Graph * graph, double minCov)$/;"	f
removeLowCoverageNodesAndDenounceDubiousReads	graphStats.c	/^boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,$/;"	f
removeMissingStrain	graphStats.c	/^void removeMissingStrain(Graph * graph, Category cat)$/;"	f
removeNextNodeFromDHeap	dfibHeap.c	/^Node *removeNextNodeFromDHeap(DFibHeap * heap)$/;"	f
removeNextNodeFromHeap	fibHeap.c	/^struct node_st *removeNextNodeFromHeap(FibHeap * heap)$/;"	f
removePreArcFromList_pg	preGraph.c	/^void removePreArcFromList_pg(PreArcI preArc, IDnum preNodeID,$/;"	f
removeReferenceMarkers	graphStats.c	/^void removeReferenceMarkers(Graph * graph, IDnum firstStrain)$/;"	f
removeShortReads	graphStats.c	/^void removeShortReads(Graph * graph)$/;"	f
removeStrainMarkers	graphStats.c	/^void removeStrainMarkers(Node * node, IDnum firstStrain)$/;"	f
removeUnreliableConnections	scaffold.c	/^static void removeUnreliableConnections(ReadSet * reads)$/;"	f	file:
renumberNodes	graph.c	/^void renumberNodes(Graph * graph)$/;"	f
renumberPreNodes_pg	preGraph.c	/^void renumberPreNodes_pg(PreGraph * preGraph)$/;"	f
replaceKeyInDHeap	dfibHeap.c	/^Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey)$/;"	f
replaceKeyInHeap	fibHeap.c	/^Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,$/;"	f
replaceValueInDHeap	dfibHeap.c	/^void replaceValueInDHeap(DFibHeapNode * node, Node * newValue)$/;"	f
replaceValueInHeap	fibHeap.c	/^void replaceValueInHeap(FibHeapNode * node, Node * newValue)$/;"	f
resetKeyFilter	kmer.c	/^void resetKeyFilter(int keyLength) {$/;"	f
resetMiniConnection	shortReadPairs.c	/^static void resetMiniConnection(Node * node, MiniConnection * localConnect,$/;"	f	file:
resetNodeStatus	graph.c	/^void resetNodeStatus(Graph * graph)$/;"	f
resetPassageMarkersStatus	graph.c	/^void resetPassageMarkersStatus(Graph * graph)$/;"	f
resetWordFilter	kmer.c	/^void resetWordFilter(int wordLength) {$/;"	f
resizeReferenceCoordinateTable	readSet.c	/^static void resizeReferenceCoordinateTable(ReferenceCoordinateTable * table, IDnum extraLength) {$/;"	f	file:
reverseCatDescriptors	graph.c	/^static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength) $/;"	f	file:
reverseComplementSequence	readSet.c	/^static void reverseComplementSequence(char * str)$/;"	f	file:
reversePushNucleotide	kmer.c	/^void reversePushNucleotide(Kmer * kmer, Nucleotide nucleotide) {$/;"	f
right	splay.c	/^	struct splayNode_st *right;$/;"	m	struct:splayNode_st	typeref:struct:splayNode_st::splayNode_st	file:
roadmap_st	roadMap.c	/^struct roadmap_st {$/;"	s	file:
scaffold	scaffold.c	/^static Connection **scaffold = NULL;$/;"	v	file:
searchForHallidayJunction	graphStats.c	/^void searchForHallidayJunction(Graph * graph)$/;"	f
seqID	splay.c	/^	IDnum seqID;$/;"	m	struct:splayNode_st	file:
sequence	tightString.c	/^	Codon *sequence;$/;"	m	struct:tString_st	file:
sequenceCategories	correctedGraph.c	/^static Category *sequenceCategories;$/;"	v	file:
sequenceCount	graph.c	/^	IDnum sequenceCount;$/;"	m	struct:graph_st	file:
sequenceCount	graph.c	/^IDnum sequenceCount(Graph * graph)$/;"	f
sequenceCount	preGraph.c	/^	IDnum sequenceCount;$/;"	m	struct:preGraph_st	file:
sequenceCount_pg	preGraph.c	/^IDnum sequenceCount_pg(PreGraph * preGraph)$/;"	f
sequenceID	passageMarker.c	/^	IDnum sequenceID;$/;"	m	struct:passage_st	file:
sequenceID	roadMap.c	/^	IDnum sequenceID;	\/\/ 32$/;"	m	struct:annotation_st	file:
sequenceLengths	correctedGraph.c	/^static IDnum *sequenceLengths;$/;"	v	file:
sequences	readCoherentGraph.c	/^static TightString *sequences = NULL;$/;"	v	file:
setBaseCoverage	readCoherentGraph.c	/^void setBaseCoverage(double coverage)$/;"	f
setEmptyMiniConnection	shortReadPairs.c	/^static void setEmptyMiniConnection(Node * node)$/;"	f	file:
setFinishID	roadMap.c	/^void setFinishID(Annotation * annot, IDnum nodeID)$/;"	f
setFinishOffset	passageMarker.c	/^void setFinishOffset(PassageMarkerI marker, Coordinate offset)$/;"	f
setInsertLengths	graph.c	/^void setInsertLengths(Graph * graph, Category cat, Coordinate insertLength,$/;"	f
setInsertionMarkers	preGraphConstruction.c	/^setInsertionMarkers(RoadMapArray * rdmaps,$/;"	f	file:
setLocalMaxDivergence	locallyCorrectedGraph.c	/^void setLocalMaxDivergence(double value)$/;"	f
setLocalMaxGaps	locallyCorrectedGraph.c	/^void setLocalMaxGaps(int value)$/;"	f
setLocalMaxReadLength	locallyCorrectedGraph.c	/^void setLocalMaxReadLength(int value)$/;"	f
setMarker	graph.c	/^void setMarker(Node * node, PassageMarkerI marker)$/;"	f
setMaxDivergence	correctedGraph.c	/^void setMaxDivergence(double value)$/;"	f
setMaxGaps	correctedGraph.c	/^void setMaxGaps(int value)$/;"	f
setMaxReadLength	correctedGraph.c	/^void setMaxReadLength(int value)$/;"	f
setMultiplicity	graph.c	/^void setMultiplicity(Arc * arc, IDnum mult)$/;"	f
setMultiplicityCutoff	readCoherentGraph.c	/^void setMultiplicityCutoff(int value)$/;"	f
setMultiplicity_pg	preGraph.c	/^void setMultiplicity_pg(PreArcI preArc, IDnum mult)$/;"	f
setNextInNode	passageMarker.c	/^void setNextInNode(PassageMarkerI marker, PassageMarkerI next)$/;"	f
setNextInSequence	passageMarker.c	/^void setNextInSequence(PassageMarkerI previous, PassageMarkerI next)$/;"	f
setNextPreArc_pg	preGraph.c	/^static void setNextPreArc_pg(PreArcI preArc, IDnum preNodeID,$/;"	f	file:
setNodeDHeapNode	correctedGraph.c	/^static void setNodeDHeapNode(Node * node, DFibHeapNode * dheapNode)$/;"	f	file:
setNodePrevious	correctedGraph.c	/^static void setNodePrevious(Node * previousNode, Node * node)$/;"	f	file:
setNodeStatus	graph.c	/^void setNodeStatus(Node * node, boolean status)$/;"	f
setNodeTime	correctedGraph.c	/^static void setNodeTime(Node * node, Time time)$/;"	f	file:
setNodeTime	locallyCorrectedGraph.c	/^static void setNodeTime(Node * node, Time time)$/;"	f	file:
setOriginalVirtualCoverage	graph.c	/^void setOriginalVirtualCoverage(Node * node, Category category,$/;"	f
setPassageMarkerFinish	passageMarker.c	/^void setPassageMarkerFinish(PassageMarkerI marker, Coordinate finish)$/;"	f
setPassageMarkerStart	passageMarker.c	/^void setPassageMarkerStart(PassageMarkerI marker, Coordinate start)$/;"	f
setPassageMarkerStatus	passageMarker.c	/^void setPassageMarkerStatus(PassageMarkerI marker, boolean status)$/;"	f
setPreNodeDescriptor_pg	preGraph.c	/^void setPreNodeDescriptor_pg(Descriptor * descr, Coordinate length, IDnum preNodeID, PreGraph * preGraph) {$/;"	f
setPreviousInSequence	passageMarker.c	/^void setPreviousInSequence(PassageMarkerI previous, PassageMarkerI next)$/;"	f
setProgramName	utility.c	/^void setProgramName(const char *name)$/;"	f
setShortReadMarkerOffset	graph.c	/^inline void setShortReadMarkerOffset(ShortReadMarker * marker,$/;"	f
setShortReadMarkerPosition	graph.c	/^inline void setShortReadMarkerPosition(ShortReadMarker * marker,$/;"	f
setSingleNodeStatus	graph.c	/^void setSingleNodeStatus(Node * node, boolean status)$/;"	f
setStartID	roadMap.c	/^void setStartID(Annotation * annot, IDnum nodeID)$/;"	f
setStartOffset	passageMarker.c	/^void setStartOffset(PassageMarkerI marker, Coordinate offset)$/;"	f
setTightStringLength	tightString.c	/^void setTightStringLength(TightString * tString, Coordinate length)$/;"	f
setTopOfTheNode	passageMarker.c	/^void setTopOfTheNode(PassageMarkerI marker)$/;"	f
setUniqueness	graph.c	/^void setUniqueness(Node * node, boolean value)$/;"	f
setUnreliableConnectionCutoff	scaffold.c	/^void setUnreliableConnectionCutoff(int val)$/;"	f
setVirtualCoverage	graph.c	/^void setVirtualCoverage(Node * node, Category category,$/;"	f
shareReadStarts	graph.c	/^void shareReadStarts(Node * target, Node * source, Graph * graph)$/;"	f
shiftRight	kmer.c	/^static void shiftRight(Kmer * kmer) {$/;"	f	file:
shortReadMarker_st	graph.c	/^struct shortReadMarker_st {$/;"	s	file:
simpleArcCount	graph.c	/^int simpleArcCount(Node * node)$/;"	f
simplePreArcCount_pg	preGraph.c	/^char simplePreArcCount_pg(IDnum preNodeID, PreGraph * preGraph)$/;"	f
simplifyNode	correctedGraph.c	/^static void simplifyNode(Node * node)$/;"	f	file:
simplifyReads	readSet.c	/^void simplifyReads(ReadSet * readSet)$/;"	f
slowPath	correctedGraph.c	/^static PassageMarkerI slowPath;$/;"	v	file:
slowPath	locallyCorrectedGraph.c	/^static PassageMarkerI slowPath;$/;"	v	file:
slowSequence	correctedGraph.c	/^static TightString *slowSequence;$/;"	v	file:
slowSequence	locallyCorrectedGraph.c	/^static TightString *slowSequence;$/;"	v	file:
slowToFastMapping	correctedGraph.c	/^static Coordinate *slowToFastMapping;$/;"	v	file:
smallNodeListMemory	graphReConstruction.c	/^static RecycleBin *smallNodeListMemory = NULL;$/;"	v	file:
smallNodeList_st	graphReConstruction.c	/^struct smallNodeList_st {$/;"	s	file:
sortGapMarkers	graph.c	/^void sortGapMarkers(Graph * graph)$/;"	f
sortKmerOccurenceTable	kmerOccurenceTable.c	/^void sortKmerOccurenceTable(KmerOccurenceTable * table) {$/;"	f
sortNodeArcs	graph.c	/^static void sortNodeArcs(Node * node)$/;"	f	file:
sortNodeGapMarkers	graph.c	/^static void sortNodeGapMarkers(Node * node, Graph * graph)$/;"	f	file:
sortReferenceCoordinateTable	readSet.c	/^static void sortReferenceCoordinateTable(ReferenceCoordinateTable * table) {$/;"	f	file:
splayNode_st	splay.c	/^struct splayNode_st {$/;"	s	file:
splayTable_st	splayTable.c	/^struct splayTable_st {$/;"	s	file:
splitNodeDescriptor	graph.c	/^void splitNodeDescriptor(Node * source, Node * target, Coordinate offset)$/;"	f
spreadReadIDs	graph.c	/^void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,$/;"	f
start	graphReConstruction.c	/^	IDnum start;$/;"	m	struct:nodeMask_st	file:
start	graphStats.c	/^	IDnum start;$/;"	m	struct:refMap_st	file:
start	graphStats.c	/^	IDnum start;$/;"	m	struct:referenceCoord_st	file:
start	locallyCorrectedGraph.c	/^static Node *start;$/;"	v	file:
start	passageMarker.c	/^	IDnum start;$/;"	m	struct:passage_st	file:
start	readSet.c	/^	Coordinate start;$/;"	m	struct:referenceCoordinate_st	file:
start	roadMap.c	/^	union positionPtr start;	\/\/ 32$/;"	m	struct:annotation_st	typeref:union:annotation_st::positionPtr	file:
startingNode	correctedGraph.c	/^static Node *startingNode;$/;"	v	file:
status	graph.c	/^	boolean status;		\/\/ 8$/;"	m	struct:node_st	file:
status	passageMarker.c	/^	boolean status;$/;"	m	struct:passage_st	file:
strainMarkerCount	graphStats.c	/^IDnum strainMarkerCount(Node * node, IDnum firstStrain)$/;"	f
surveyPath	graphStats.c	/^static void surveyPath(PassageMarkerI marker)$/;"	f	file:
surveyPaths	graphStats.c	/^void surveyPaths(Graph * graph)$/;"	f
swap	dfib.c	73;"	d	file:
swap	fib.c	69;"	d	file:
tString_st	tightString.c	/^struct tString_st {$/;"	s	file:
table	splayTable.c	/^	SplayTree **table;$/;"	m	struct:splayTable_st	file:
tableLocks	splayTable.c	/^	omp_lock_t *tableLocks;$/;"	m	struct:splayTable_st	file:
terminalReferenceMarker	graphStats.c	/^static boolean terminalReferenceMarker(Node * node, ReadSet * reads) {$/;"	f	file:
test	splay.c	/^int test(int argc, char **argv)$/;"	f
testConnection	scaffold.c	/^static boolean testConnection(IDnum IDA, Connection * connect,$/;"	f	file:
testForBizarreMarkers	graphStats.c	/^void testForBizarreMarkers(Graph * graph)$/;"	f
test_lock	concatenatedPreGraph.c	/^static boolean test_lock(IDnum index) {$/;"	f	file:
threadSequenceThroughGraph	graphReConstruction.c	/^static void threadSequenceThroughGraph(TightString * tString,$/;"	f	file:
ticketMemory	correctedGraph.c	/^static RecycleBin *ticketMemory;$/;"	v	file:
ticketQueue	correctedGraph.c	/^static Ticket *ticketQueue;$/;"	v	file:
times	correctedGraph.c	/^static Time *times;$/;"	v	file:
times	locallyCorrectedGraph.c	/^static Time *times;$/;"	v	file:
tkt_st	correctedGraph.c	/^struct tkt_st {$/;"	s	file:
todo	correctedGraph.c	/^static Ticket **todo;$/;"	v	file:
todoLists	correctedGraph.c	/^static Ticket **todoLists;$/;"	v	file:
totalAssemblyLength	graphStats.c	/^Coordinate totalAssemblyLength(Graph * graph)$/;"	f
totalGraphLength	graphStats.c	/^Coordinate totalGraphLength(Graph * graph)$/;"	f
tourBus	correctedGraph.c	/^static void tourBus(Node * startingPoint)$/;"	f	file:
tourBusArc	correctedGraph.c	/^static void tourBusArc(Node * origin, Arc * arc, Time originTime)$/;"	f	file:
tourBusArc_local	locallyCorrectedGraph.c	/^static void tourBusArc_local(Node * origin, Arc * arc, Time originTime)$/;"	f	file:
tourBusNode	correctedGraph.c	/^static void tourBusNode(Node * node)$/;"	f	file:
tourBusNode_local	locallyCorrectedGraph.c	/^static void tourBusNode_local(Node * node)$/;"	f	file:
tourBus_local	locallyCorrectedGraph.c	/^static void tourBus_local(Node * startingPoint)$/;"	f	file:
transferNodeData	correctedGraph.c	/^static void transferNodeData(Node * source, Node * target)$/;"	f	file:
transposePassageMarker	passageMarker.c	/^void transposePassageMarker(PassageMarkerI marker, Node * node)$/;"	f
treeMemory	splay.c	/^static RecycleBin *treeMemory = NULL;$/;"	v	file:
trimLongReadTips	readCoherentGraph.c	/^static void trimLongReadTips()$/;"	f	file:
trimTightString	tightString.c	/^void trimTightString(TightString * tString, Coordinate length)$/;"	f
trimTightStringArray	tightString.c	/^void trimTightStringArray(TightString ** array, IDnum sequenceCount,$/;"	f
trimTightStringArraySanger	tightString.c	/^void trimTightStringArraySanger(TightString ** array, IDnum sequenceCount,$/;"	f
twin	scaffold.c	/^	Connection *twin;$/;"	m	struct:connection_st	file:
twinArc	graph.c	/^	Arc *twinArc;		\/\/ 64$/;"	m	struct:arc_st	file:
twinMarker	passageMarker.c	/^	PassageMarkerI twinMarker;$/;"	m	struct:passage_st	file:
twinNode	graph.c	/^	Node *twinNode;		\/\/ 64$/;"	m	struct:node_st	file:
unLockNode	graphReConstruction.c	/^static inline void unLockNode(Node *node)$/;"	f	file:
uniqueNodesConnect	readCoherentGraph.c	/^static boolean uniqueNodesConnect(Node * startingNode)$/;"	f	file:
uniqueness	graph.c	/^	boolean uniqueness;	\/\/ 8$/;"	m	struct:node_st	file:
unlockMemorizedNodes	graphReConstruction.c	/^static void unlockMemorizedNodes(SmallNodeList ** nodePile)$/;"	f	file:
unmarkInterestingNodes	shortReadPairs.c	/^static void unmarkInterestingNodes()$/;"	f	file:
unmarkNode	shortReadPairs.c	/^void unmarkNode(Node * node, MiniConnection * localConnect)$/;"	f
updateMarkers	graphStats.c	/^static void updateMarkers(PassageMarkerList * list)$/;"	f	file:
updateMembers	readCoherentGraph.c	/^static void updateMembers(Node * bypass, Node * nextNode)$/;"	f	file:
updateNodeStatus	correctedGraph.c	/^static void updateNodeStatus(Node * node)$/;"	f	file:
updatePreArcData_pg	preGraph.c	/^static void updatePreArcData_pg(PreArcI preArc, IDnum oldPreNodeID,$/;"	f	file:
usedReads	graphStats.c	/^IDnum usedReads(Graph * graph, Coordinate minContigLength) $/;"	f
variance	scaffold.c	/^	double variance;$/;"	m	struct:connection_st	file:
variance	shortReadPairs.c	/^	double variance;$/;"	m	struct:miniConnection_st	file:
velvetLog	utility.c	/^void velvetLog(const char *format, ...)$/;"	f
velvetifySequence	readSet.c	/^static void velvetifySequence(char * str) {$/;"	f	file:
virtualCoverage	graph.c	/^	IDnum virtualCoverage[CATEGORIES];	\/\/ 32 * 2$/;"	m	struct:node_st	file:
wordLength	graph.c	/^	int wordLength;$/;"	m	struct:graph_st	file:
wordLength	preGraph.c	/^	int wordLength;$/;"	m	struct:preGraph_st	file:
writeFastaSequence	readSet.c	/^static void writeFastaSequence(FILE * outfile, const char * str)$/;"	f	file:
writeNucleotide	tightString.c	/^void writeNucleotide(Nucleotide nucleotide, Codon * codonPtr, int position)$/;"	f
writeNucleotideAtPosition	tightString.c	/^writeNucleotideAtPosition(Nucleotide nucleotide, Coordinate position,$/;"	f
writeNucleotideInDescriptor	graph.c	/^static void writeNucleotideInDescriptor(Nucleotide nucleotide,$/;"	f	file:
writeNucleotideInDescriptor_pg	preGraph.c	/^static void writeNucleotideInDescriptor_pg(Nucleotide nucleotide,$/;"	f	file:
writeNucleotideNumber	tightString.c	/^writeNucleotideNumber(Nucleotide nucleotide, Codon * codonPtr,$/;"	f
