!_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	5.8	//
ADENINE	binarySequences.c	335;"	d	file:
ADENINE	graph.c	33;"	d	file:
ADENINE	graphReConstruction.c	43;"	d	file:
ADENINE	preGraph.c	38;"	d	file:
ADENINE	preGraphConstruction.c	40;"	d	file:
ATTRIBUTE	utility.h	25;"	d
ATTRIBUTE	utility.h	27;"	d
ATTRIBUTE_PACKED	correctedGraph.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:tkt_st
ATTRIBUTE_PACKED	dfibpriv.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:dfibheap
ATTRIBUTE_PACKED	dfibpriv.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:dfibheap_el
ATTRIBUTE_PACKED	globals.h	34;"	d
ATTRIBUTE_PACKED	globals.h	36;"	d
ATTRIBUTE_PACKED	graph.c	/^}  ATTRIBUTE_PACKED;	\/\/ 352 Total$/;"	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;$/;"	v	typeref:struct:referenceCoord_st
ATTRIBUTE_PACKED	kmer.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:kmer_st
ATTRIBUTE_PACKED	kmerOccurenceTable.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:kmerOccurence_st
ATTRIBUTE_PACKED	locallyCorrectedGraph.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:nodeList_st
ATTRIBUTE_PACKED	passageMarker.c	/^} ATTRIBUTE_PACKED;$/;"	v	typeref:struct:passage_st
ATTRIBUTE_PACKED	passageMarker.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:passageList_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.h	/^}  ATTRIBUTE_PACKED;$/;"	v	typeref:struct:tString_st
Adenine	tightString.c	/^static const Nucleotide Adenine = 0;$/;"	v	file:
AllocArray	allocArray.h	/^typedef struct AllocArray_st AllocArray;$/;"	t	typeref:struct:AllocArray_st
AllocArrayFreeElement	allocArray.h	/^typedef struct AllocArrayFreeElement_st AllocArrayFreeElement;$/;"	t	typeref:struct:AllocArrayFreeElement_st
AllocArrayFreeElement_st	allocArray.c	/^struct AllocArrayFreeElement_st$/;"	s	file:
AllocArray_st	allocArray.h	/^struct AllocArray_st$/;"	s
Annotation	globals.h	/^typedef struct annotation_st Annotation;$/;"	t	typeref:struct:annotation_st
AnnotationList	globals.h	/^typedef struct annotationList_st AnnotationList;$/;"	t	typeref:struct:annotationList_st
Arc	globals.h	/^typedef struct arc_st Arc;$/;"	t	typeref:struct:arc_st
Arc	run.c	26;"	d	file:
ArrayIdx	globals.h	/^typedef uint32_t ArrayIdx;$/;"	t
ArrayIdx	globals.h	/^typedef uint64_t ArrayIdx;$/;"	t
BACKTRACK_CUTOFF	shortReadPairs.c	38;"	d	file:
BAM	readSet.c	1418;"	d	file:
BLOCKSIZE	dfib.c	57;"	d	file:
BLOCKSIZE	fib.c	57;"	d	file:
BLOCKSIZE	graph.c	95;"	d	file:
BLOCKSIZE	graphReConstruction.c	149;"	d	file:
BLOCKSIZE	readCoherentGraph.c	61;"	d	file:
BLOCKS_ALLOC_SHIFT	allocArray.c	186;"	d	file:
BLOCKS_ALLOC_SIZE	allocArray.c	34;"	d	file:
BLOCKS_ALLOC_SIZE	allocArray.c	37;"	d	file:
BLOCK_SIZE	scaffold.c	41;"	d	file:
BLOCK_SIZE	shortReadPairs.c	36;"	d	file:
BUFFER_SIZE	splayTable.c	181;"	d	file:
BUFFER_SIZE	splayTable.c	68;"	d	file:
CHARS	kmer.c	41;"	d	file:
CHUNKSIZE	splay.c	33;"	d	file:
CYTOSINE	binarySequences.c	336;"	d	file:
CYTOSINE	graph.c	34;"	d	file:
CYTOSINE	graphReConstruction.c	44;"	d	file:
CYTOSINE	preGraph.c	39;"	d	file:
CYTOSINE	preGraphConstruction.c	41;"	d	file:
Category	globals.h	/^typedef int8_t Category;$/;"	t
Chunk	recycleBin.c	/^} Chunk;$/;"	t	typeref:struct:chunk_st	file:
CnyUnifiedSeqFileHeader	binarySequences.h	/^} CnyUnifiedSeqFileHeader;$/;"	t	typeref:struct:__anon1
Codon	tightString.h	/^typedef unsigned char Codon;$/;"	t
Connection	scaffold.h	/^typedef struct connection_st Connection;$/;"	t	typeref:struct:connection_st
ConnectionStack	scaffold.c	/^typedef struct ConnectionStack_st ConnectionStack;$/;"	t	typeref:struct:ConnectionStack_st	file:
ConnectionStack_st	scaffold.c	/^struct ConnectionStack_st$/;"	s	file:
Coordinate	globals.h	/^typedef int64_t Coordinate;$/;"	t
Cytosine	tightString.c	/^static const Nucleotide Cytosine = 1;$/;"	v	file:
DECLARE_FAST_ACCESSORS	allocArray.h	59;"	d
DECLARE_FAST_ACCESSORS	preGraph.c	/^DECLARE_FAST_ACCESSORS(PREARC, PreArc, preArcMemory)$/;"	f
DFibHeap	globals.h	/^typedef struct dfibheap DFibHeap;$/;"	t	typeref:struct:dfibheap
DFibHeapNode	globals.h	/^typedef struct dfibheap_el DFibHeapNode;$/;"	t	typeref:struct:dfibheap_el
DOTNode	graph.c	/^void DOTNode(Node * node, FILE * outfile)$/;"	f
Descriptor	globals.h	/^typedef uint8_t Descriptor;$/;"	t
FASTA	readSet.c	1414;"	d	file:
FASTA_GZ	readSet.c	1415;"	d	file:
FASTQ	readSet.c	1413;"	d	file:
FASTQ_GZ	readSet.c	1416;"	d	file:
FAST_TO_SLOW	correctedGraph.c	2085;"	d	file:
FILTER0	tightString.c	/^static const Codon FILTER0 = ~((Codon) 3);$/;"	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);$/;"	v	file:
FibHeap	globals.h	/^typedef struct fibheap FibHeap;$/;"	t	typeref:struct:fibheap
FibHeapNode	globals.h	/^typedef struct fibheap_el FibHeapNode;$/;"	t	typeref:struct:fibheap_el
Fmatrix	correctedGraph.c	/^static double **Fmatrix;$/;"	v	file:
Fmatrix	locallyCorrectedGraph.c	/^static double **Fmatrix;$/;"	v	file:
FormattedWriter	utility.h	/^} FormattedWriter;$/;"	t	typeref:struct:formattedWriter_st
GAPBLOCKSIZE	graph.c	96;"	d	file:
GUANINE	binarySequences.c	337;"	d	file:
GUANINE	graph.c	35;"	d	file:
GUANINE	graphReConstruction.c	45;"	d	file:
GUANINE	preGraph.c	40;"	d	file:
GUANINE	preGraphConstruction.c	42;"	d	file:
GapMarker	globals.h	/^typedef struct gapMarker_st GapMarker;$/;"	t	typeref:struct:gapMarker_st
Graph	globals.h	/^typedef struct graph_st Graph;$/;"	t	typeref:struct:graph_st
Guanine	tightString.c	/^static const Nucleotide Guanine = 2;$/;"	v	file:
HASH_BUCKETS_NB	splayTable.c	63;"	d	file:
ID	graph.c	/^	IDnum ID;		\/\/ 32$/;"	m	struct:node_st	file:
IDnum	globals.h	/^typedef int32_t IDnum;$/;"	t
IDnum	globals.h	/^typedef int64_t IDnum;$/;"	t
INCLUDED_RECYCLEBIN_H	recycleBin.h	37;"	d
INDEL	correctedGraph.c	/^static const Time INDEL = 0;$/;"	v	file:
INDEL	locallyCorrectedGraph.c	/^static const Time INDEL = 0;$/;"	v	file:
INDEX_LENGTH	allocArray.c	41;"	d	file:
INDEX_LENGTH	allocArray.c	43;"	d	file:
INTS	kmer.c	42;"	d	file:
INT_BITS	dfib.c	81;"	d	file:
INT_BITS	fib.c	77;"	d	file:
INVALID	binarySequences.c	339;"	d	file:
InsertionMarker	globals.h	/^typedef struct insertionMarker_st InsertionMarker;$/;"	t	typeref:struct:insertionMarker_st
KMER_BYTE_SIZE	kmer.h	49;"	d
KMER_BYTE_SIZE	kmer.h	51;"	d
KMER_CHARS	kmer.h	56;"	d
KMER_INTS	kmer.h	55;"	d
KMER_LONGLONGS	kmer.h	53;"	d
KMER_LONGS	kmer.h	54;"	d
KMER_QUOTIENT	kmer.h	46;"	d
KMER_REMAINDER	kmer.h	47;"	d
Kmer	globals.h	/^typedef struct kmer_st Kmer;$/;"	t	typeref:struct:kmer_st
KmerKey	globals.h	/^typedef uint64_t KmerKey;$/;"	t
KmerOccurence	globals.h	/^typedef struct kmerOccurence_st KmerOccurence;$/;"	t	typeref:struct:kmerOccurence_st
KmerOccurenceTable	globals.h	/^typedef struct kmerOccurenceTable_st KmerOccurenceTable;$/;"	t	typeref:struct:kmerOccurenceTable_st
LISTBLOCKSIZE	passageMarker.c	/^static const int LISTBLOCKSIZE = 10000;$/;"	v	file:
LN2	readCoherentGraph.c	34;"	d	file:
LN2	scaffold.c	42;"	d	file:
LN2	shortReadPairs.c	37;"	d	file:
LONG	globals.h	45;"	d
LONGLONGS	kmer.c	44;"	d	file:
LONGS	kmer.c	43;"	d	file:
LONG_NODE_CUTOFF	readCoherentGraph.c	33;"	d	file:
LONG_PAIRED	globals.h	46;"	d
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:
MAXLINE	globals.h	43;"	d
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;$/;"	v	file:
Mask	globals.h	/^typedef struct mask_st Mask;$/;"	t	typeref:struct:mask_st
MiniConnection	shortReadPairs.c	/^typedef struct miniConnection_st MiniConnection;$/;"	t	typeref:struct:miniConnection_st	file:
NB_PAGES_ALLOC	allocArray.c	33;"	d	file:
NB_PAGES_ALLOC	allocArray.c	36;"	d	file:
NB_PUSH	splayTable.c	67;"	d	file:
NULL	globals.h	25;"	d
NULL	roadMap.c	34;"	d	file:
NULL_IDX	globals.h	50;"	d
Node	globals.h	/^typedef struct node_st Node;$/;"	t	typeref:struct:node_st
NodeList	globals.h	/^typedef struct nodeList_st NodeList;$/;"	t	typeref:struct:nodeList_st
NodeMask	graphReConstruction.c	/^typedef struct nodeMask_st NodeMask;$/;"	t	typeref:struct:nodeMask_st	file:
Nucleotide	globals.h	/^typedef int8_t Nucleotide;$/;"	t
PEBBLE_ROUND_NUM	scaffold.c	/^static int PEBBLE_ROUND_NUM = 0;$/;"	v	file:
PROBABILITY_CUTOFF	readCoherentGraph.c	35;"	d	file:
PassageMarker	passageMarker.c	/^typedef struct passage_st PassageMarker;$/;"	t	typeref:struct:passage_st	file:
PassageMarkerI	globals.h	/^typedef ArrayIdx PassageMarkerI;$/;"	t
PassageMarkerList	globals.h	/^typedef struct passageList_st PassageMarkerList;$/;"	t	typeref:struct:passageList_st
PreArc	preGraph.c	/^typedef struct preArc_st PreArc;$/;"	t	typeref:struct:preArc_st	file:
PreArcI	globals.h	/^typedef ArrayIdx PreArcI;$/;"	t
PreGraph	globals.h	/^typedef struct preGraph_st PreGraph;$/;"	t	typeref:struct:preGraph_st
PreMarker	globals.h	/^typedef struct preMarker_st PreMarker;$/;"	t	typeref:struct:preMarker_st
PreNode	globals.h	/^typedef struct preNode_st PreNode;$/;"	t	typeref:struct:preNode_st
Probability	globals.h	/^typedef double Probability;$/;"	t
Quality	globals.h	/^typedef uint8_t Quality;$/;"	t
RAW	readSet.c	1419;"	d	file:
RAW_GZ	readSet.c	1420;"	d	file:
RBConnection	readCoherentGraph.c	/^typedef struct rb_connection_st RBConnection;$/;"	t	typeref:struct:rb_connection_st	file:
READS_PER_LOCK	scaffold.c	78;"	d	file:
REFERENCE	globals.h	47;"	d
RELEASE_NUMBER	globals.h	40;"	d
ReadOccurence	scaffold.c	/^typedef struct readOccurence_st ReadOccurence;$/;"	t	typeref:struct:readOccurence_st	file:
ReadSet	globals.h	/^typedef struct readSet_st ReadSet;$/;"	t	typeref:struct:readSet_st
ReadStart	globals.h	/^typedef struct readStart_st ReadStart;$/;"	t	typeref:struct:readStart_st
RecycleBin	recycleBin.h	/^typedef struct recycleBin_st RecycleBin;$/;"	t	typeref:struct:recycleBin_st
RecycleBin_Node	recycleBin.c	/^typedef struct RecycleBin_Node {$/;"	s	file:
RecycleBin_Node	recycleBin.c	/^} RecycleBin_Node;$/;"	t	typeref:struct:RecycleBin_Node	file:
RefInfo	binarySequences.h	/^typedef struct refInfo_st RefInfo;$/;"	t	typeref:struct:refInfo_st
RefInfoList	binarySequences.h	/^typedef struct refInfoList_st RefInfoList;$/;"	t	typeref:struct:refInfoList_st
ReferenceCoord	graphStats.c	/^typedef struct referenceCoord_st ReferenceCoord;$/;"	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; $/;"	t	typeref:struct:refMap_st	file:
RoadMap	globals.h	/^typedef struct roadmap_st RoadMap;$/;"	t	typeref:struct:roadmap_st
RoadMapArray	globals.h	/^typedef struct roadMapArray_st RoadMapArray;$/;"	t	typeref:struct:roadMapArray_st
SAM	readSet.c	1417;"	d	file:
SET_BINARY_MODE	binarySequences.c	43;"	d	file:
SET_BINARY_MODE	binarySequences.c	45;"	d	file:
SET_BINARY_MODE	readSet.c	46;"	d	file:
SET_BINARY_MODE	readSet.c	48;"	d	file:
SHORT_NUCL_LENGTH	binarySequences.c	52;"	d	file:
SIM	correctedGraph.c	/^static const Time SIM[4][4] = {$/;"	v	file:
SIM	locallyCorrectedGraph.c	/^static const Time SIM[4][4] = {$/;"	v	file:
SLOW_TO_FAST	correctedGraph.c	2084;"	d	file:
SequenceReader	globals.h	/^typedef struct sequenceReader_st SequenceReader;$/;"	t	typeref:struct:sequenceReader_st
SequencesReader	globals.h	/^typedef struct sequencesReader_st SequencesReader;$/;"	t	typeref:struct:sequencesReader_st
SequencesWriter	binarySequences.h	/^typedef struct sequencesWriter_st SequencesWriter;$/;"	t	typeref:struct:sequencesWriter_st
ShortLength	globals.h	/^typedef int16_t ShortLength;$/;"	t
ShortLength	globals.h	/^typedef int32_t ShortLength;$/;"	t
ShortReadMarker	globals.h	/^typedef struct shortReadMarker_st ShortReadMarker;$/;"	t	typeref:struct:shortReadMarker_st
SingleRotateWithLeft	splay.c	/^static SplayNode *SingleRotateWithLeft(SplayNode * K2)$/;"	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:
SplayTable	globals.h	/^typedef struct splayTable_st SplayTable;$/;"	t	typeref:struct:splayTable_st
SplayTree	splay.c	/^typedef struct splayNode_st SplayTree;$/;"	t	typeref:struct:splayNode_st	file:
SplayTree	splay.h	/^typedef struct splayNode_st SplayTree;$/;"	t	typeref:struct:splayNode_st
StringBuffer	utility.h	/^StringBuffer;$/;"	t	typeref:struct:__anon2
THYMINE	binarySequences.c	338;"	d	file:
THYMINE	graph.c	36;"	d	file:
THYMINE	graphReConstruction.c	46;"	d	file:
THYMINE	preGraph.c	41;"	d	file:
THYMINE	preGraphConstruction.c	43;"	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:
TightString	globals.h	/^typedef struct tString_st TightString;$/;"	t	typeref:struct:tString_st
Time	globals.h	/^typedef double Time;$/;"	t
UNDEFINED	kmer.c	40;"	d	file:
UNRELIABLE_CONNECTION_CUTOFF	scaffold.c	/^static IDnum UNRELIABLE_CONNECTION_CUTOFF = 5;$/;"	v	file:
UPDATE_NUMBER	globals.h	41;"	d
USF_READ_BUF_SIZE	binarySequences.h	72;"	d
UTILITY_H_	utility.h	22;"	d
VERSION_NUMBER	globals.h	39;"	d
Variant	graphStats.c	/^} Variant;$/;"	t	typeref:struct:variant_st	file:
WORDLENGTH	correctedGraph.c	/^static int WORDLENGTH;$/;"	v	file:
WORDLENGTH	locallyCorrectedGraph.c	/^static int WORDLENGTH;$/;"	v	file:
WORDLENGTH	roadMap.h	/^	int WORDLENGTH;$/;"	m	struct:roadMapArray_st
WORDLENGTH	splayTable.c	/^	int WORDLENGTH;$/;"	m	struct:splayTable_st	file:
WRITE_BUF_MASK	binarySequences.c	51;"	d	file:
WRITE_BUF_SHFT	binarySequences.c	49;"	d	file:
WRITE_BUF_SIZE	binarySequences.c	50;"	d	file:
_ALLOC_ARRAY_H_	allocArray.h	23;"	d
_BINARYSEQUENCES_H_	binarySequences.h	22;"	d
_CONCATENATEDGRAPH_H_	concatenatedGraph.h	22;"	d
_CONCATENATEDPREGRAPH_H_	concatenatedPreGraph.h	22;"	d
_CORRECTEDGRAPH_H_	correctedGraph.h	22;"	d
_DFIBHEAP_H_	dfibHeap.h	22;"	d
_DFIBPRIV_H_	dfibpriv.h	51;"	d
_DFIB_H_	dfib.h	51;"	d
_FIBHEAP_H_	fibHeap.h	22;"	d
_FIBPRIV_H_	fibpriv.h	51;"	d
_FIB_H_	fib.h	51;"	d
_GLOBALS_H_	globals.h	22;"	d
_GRAPHRECONSTRUCTION_H_	graphReConstruction.h	22;"	d
_GRAPHSTATS_H_	graphStats.h	22;"	d
_GRAPH_H_	graph.h	22;"	d
_KMEROCCURENCETABLE_H_	kmerOccurenceTable.h	22;"	d
_KMER_H_	kmer.h	22;"	d
_LOCALLYCORRECTEDGRAPH_H_	locallyCorrectedGraph.h	22;"	d
_PASSAGEMARKER_H_	passageMarker.h	22;"	d
_PREGRAPHCONSTRUCTION_H_	preGraphConstruction.h	22;"	d
_PREGRAPH_H_	preGraph.h	22;"	d
_READCOHERENTGRAPH_H_	readCoherentGraph.h	22;"	d
_READSET_H_	readSet.h	22;"	d
_ROADMAP_H_	roadMap.h	22;"	d
_SCAFFOLD_H_	scaffold.h	22;"	d
_SHORTREADPAIRS_H_	shortReadPairs.h	22;"	d
_SPLAYTABLE_H_	splayTable.h	22;"	d
_Splay_H	splay.h	22;"	d
_TIGHTSTRING_H_	tightString.h	22;"	d
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)$/;"	f
addMapping	readSet.c	/^static void addMapping(boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {$/;"	f	file:
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,$/;"	f
addReadsToGraph	graphReConstruction.c	/^static void addReadsToGraph(TightString * tString,$/;"	f	file:
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, Coordinate nodeLength)$/;"	f	file:
adjustShortReads	readCoherentGraph.c	/^static void adjustShortReads(Node * target, PassageMarkerI pathMarker)$/;"	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)$/;"	f	file:
advanceCnySeqCurrentRead	binarySequences.c	/^boolean advanceCnySeqCurrentRead(SequencesReader *seqReadInfo)$/;"	f
alignCnySeqToNextByteBoundary	binarySequences.c	/^static void alignCnySeqToNextByteBoundary(SequencesWriter *seqWriteInfo)$/;"	f	file:
allocArrayAllocate	allocArray.c	/^allocArrayAllocate (AllocArray *array)$/;"	f
allocArrayArrayAllocate	allocArray.c	/^ArrayIdx allocArrayArrayAllocate(AllocArray *array)$/;"	f
allocArrayArrayFree	allocArray.c	/^allocArrayArrayFree(AllocArray *array, ArrayIdx idx)$/;"	f
allocArrayFree	allocArray.c	/^allocArrayFree (AllocArray *array, ArrayIdx idx)$/;"	f
allocArrayGetElement	allocArray.c	/^allocArrayGetElement (AllocArray *array, ArrayIdx idx)$/;"	f	file:
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()$/;"	f	file:
allocateConnectionStack	scaffold.c	/^static ConnectionStack *allocateConnectionStack(void)$/;"	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
allocateMask	graphStats.c	/^static Mask *allocateMask()$/;"	f	file:
allocateMask	readSet.c	/^static Mask *allocateMask(SequencesWriter *seqWriteInfo)$/;"	f	file:
allocateMask	splayTable.c	/^static Mask *allocateMask()$/;"	f	file:
allocateNode	graph.c	/^Node *allocateNode()$/;"	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:
allocated	utility.h	/^	size_t allocated;$/;"	m	struct:__anon2
annot	preGraphConstruction.c	/^	Annotation *annot;$/;"	m	struct:insertionMarker_st	file:
annotationBuffer	splayTable.c	/^StringBuffer *annotationBuffer = NULL;$/;"	v
annotationBuffer	splayTable.c	/^static StringBuffer **annotationBuffer = NULL;$/;"	v	file:
annotationBufferW	splayTable.c	/^static StringBuffer **annotationBufferW = NULL;$/;"	v	file:
annotationCount	roadMap.c	/^	ShortLength annotationCount;$/;"	m	struct:roadmap_st	file:
annotationOffset	preGraphConstruction.c	/^Coordinate *annotationOffset = NULL;$/;"	v
annotation_st	roadMap.c	/^struct annotation_st {$/;"	s	file:
annotations	roadMap.h	/^	Annotation *annotations;$/;"	m	struct:roadMapArray_st
appendDescriptors	graph.c	/^void appendDescriptors(Node * destination, Node * source)$/;"	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
appendLine	splayTable.c	/^static void appendLine(char *line, int thread)$/;"	f	file:
appendNegativeDescriptor_pg	preGraph.c	/^static void appendNegativeDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {$/;"	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,$/;"	f	file:
appendStringBuffer	utility.c	/^void appendStringBuffer(StringBuffer *buffer, char *str)$/;"	f
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:
array	roadMap.h	/^	RoadMap *array;$/;"	m	struct:roadMapArray_st
arrayLength	readSet.c	/^	IDnum arrayLength;$/;"	m	struct:referenceCoordinateTable_st	file:
backReference	shortReadPairs.c	/^	Connection *backReference;$/;"	m	struct:miniConnection_st	file:
blockSize	allocArray.h	/^	size_t blockSize;$/;"	m	struct:AllocArray_st
blocks	allocArray.h	/^	void **blocks;$/;"	m	struct:AllocArray_st
blurLastShortReadMarker	graph.c	/^void blurLastShortReadMarker(Node * node, Graph * graph)$/;"	f
boolean	globals.h	/^typedef int8_t boolean;$/;"	t
buffer	utility.h	/^	char * buffer;$/;"	m	struct:formattedWriter_st
bufferWritter	splayTable.c	/^static void bufferWritter(FILE *outFile)$/;"	f	file:
buffer_size	utility.h	/^	size_t buffer_size;$/;"	m	struct:formattedWriter_st
buildScaffold	scaffold.c	/^void buildScaffold(Graph * argGraph,$/;"	f
bypass	readCoherentGraph.c	/^static Node *bypass()$/;"	f	file:
callocOrExit	utility.h	39;"	d
callocOrExit3	utility.c	/^void *callocOrExit3(size_t count, size_t size, const char *name)$/;"	f
callocOrExitWithoutCast	utility.h	49;"	d
catDescriptors	graph.c	/^static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength) $/;"	f	file:
categories	readSet.h	/^	Category *categories;$/;"	m	struct:readSet_st
ceillog2	dfib.c	/^static inline IDnum ceillog2(IDnum a)$/;"	f	file:
ceillog2	fib.c	/^static inline IDnum ceillog2(IDnum a)$/;"	f	file:
charLeftFilter	kmer.c	/^static const uint8_t charLeftFilter = (uint8_t) 3 << 6; $/;"	v	file:
charWordFilter	kmer.c	/^static uint8_t charWordFilter = (uint8_t) ((int8_t) -1); $/;"	v	file:
chars	kmer.h	/^	uint8_t chars;$/;"	m	struct:kmer_st
checkNode	shortReadPairs.c	/^void checkNode(Node* node) {$/;"	f
chooseDestination	graphStats.c	/^static Node *chooseDestination(PassageMarkerList * list)$/;"	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:
clean	scaffold.c	/^	unsigned char clean;$/;"	m	struct:connection_st	file:
cleanMemory	shortReadPairs.c	/^static void cleanMemory()$/;"	f	file:
cleanScaffoldMemory	scaffold.c	/^void cleanScaffoldMemory() {$/;"	f
cleanUpMemory	preGraphConstruction.c	/^cleanUpMemory(PreGraph * preGraph, RoadMapArray * rdmaps, IDnum * chains)$/;"	f	file:
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) {$/;"	f
clipTipsHard	correctedGraph.c	/^void clipTipsHard(Graph * graph, boolean conserveLong)$/;"	f
clipTipsVeryHardLocally	locallyCorrectedGraph.c	/^static void clipTipsVeryHardLocally()$/;"	f	file:
clipTips_pg	concatenatedPreGraph.c	/^void clipTips_pg(PreGraph * preGraph)$/;"	f
closeCnySeqForWrite	binarySequences.c	/^void closeCnySeqForWrite(SequencesWriter *seqWriteInfo)$/;"	f
cnySeqHostBufferFull	binarySequences.c	/^static void cnySeqHostBufferFull(SequencesWriter *seqWriteInfo)$/;"	f	file:
cnySeqInsertEnd	binarySequences.c	/^void cnySeqInsertEnd(SequencesWriter *seqWriteInfo)$/;"	f
cnySeqInsertNucleotideString	binarySequences.c	/^void cnySeqInsertNucleotideString(const char *pReadBuf, SequencesWriter *seqWriteInfo) {$/;"	f
cnySeqInsertReferenceMask	binarySequences.c	/^void cnySeqInsertReferenceMask(SequencesWriter *seqWriteInfo, Mask *referenceMask) {$/;"	f
cnySeqInsertSequenceName	binarySequences.c	/^void cnySeqInsertSequenceName(const char *name, IDnum readID, SequencesWriter *seqWriteInfo, Category cat) {$/;"	f
cnySeqInsertStart	binarySequences.c	/^void cnySeqInsertStart(SequencesWriter *seqWriteInfo)$/;"	f
collectReferenceCoords	graphStats.c	/^static ReferenceCoord * collectReferenceCoords(SequencesReader *seqReadInfo, IDnum referenceCount) {$/;"	f	file:
column	utility.h	/^	size_t column;$/;"	m	struct:formattedWriter_st
comesFromNode	shortReadPairs.c	/^static boolean comesFromNode(PassageMarkerI marker, Node * node)$/;"	f	file:
commonLength	graphStats.c	/^Coordinate commonLength(Node * node, IDnum firstStrain)$/;"	f
commonNodeReads	graph.c	/^ShortReadMarker *commonNodeReads(Node * nodeA, Node * nodeB, Graph * graph,$/;"	f
compareCoords	graphStats.c	/^static int compareCoords(const void * A, const void * B) {$/;"	f	file:
compareIDnums	graph.c	/^static inline int compareIDnums(const void *A, const void *B)$/;"	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:
compareVariants	graphStats.c	/^static int compareVariants(const void * pA, const void * pB) {$/;"	f	file:
computeClearHSPs	splayTable.c	/^static void computeClearHSPs(TightString * array, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount, IDnum seqID) {$/;"	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:
computePartialReadToNodeMappingLong	scaffold.c	/^static void computePartialReadToNodeMappingLong(IDnum nodeID,$/;"	f	file:
computePartialReadToNodeMappingShort	scaffold.c	/^static void computePartialReadToNodeMappingShort(IDnum nodeID,$/;"	f	file:
computeReadToNodeCounts	scaffold.c	/^static IDnum *computeReadToNodeCounts(Coordinate *totalCount)$/;"	f	file:
computeReadToNodeMappings	scaffold.c	/^static ReadOccurence **computeReadToNodeMappings(IDnum * readNodeCounts,$/;"	f	file:
computeReferenceMappings	graphReConstruction.c	/^static ReferenceMapping * computeReferenceMappings(char * preGraphFilename, ReadSet * reads, Coordinate * referenceMappingLength, IDnum * referenceCount) {$/;"	f	file:
computeSecondInPair	readSet.c	/^void computeSecondInPair(ReadSet * reads)$/;"	f
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,$/;"	f	file:
concatenateNodesAndVaccinate	correctedGraph.c	/^static void concatenateNodesAndVaccinate(Node * nodeA, Node * nodeB,$/;"	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)$/;"	f
concatenatePreNodes	concatenatedPreGraph.c	/^static void concatenatePreNodes(IDnum preNodeAID, PreArcI oldPreArc,$/;"	f	file:
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)$/;"	f
concatenateTodoListIntoActive	correctedGraph.c	/^static void concatenateTodoListIntoActive(Node * nodeB)$/;"	f	file:
concatenateTodoLists	correctedGraph.c	/^static void concatenateTodoLists(Node * nodeA, Node * nodeB)$/;"	f	file:
confidenceScores	readSet.h	/^	Quality **confidenceScores;$/;"	m	struct:readSet_st
connectAnnotation	preGraphConstruction.c	/^static void connectAnnotation(IDnum * currentPreNodeID, Annotation * annot,$/;"	f	file:
connectPassageMarkers	passageMarker.c	/^connectPassageMarkers(PassageMarkerI previous, PassageMarkerI next,$/;"	f
connectPreNodeToTheNext	preGraphConstruction.c	/^static void connectPreNodeToTheNext(IDnum * currentPreNodeID,$/;"	f	file:
connectPreNodes	preGraphConstruction.c	/^static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
connection	scaffold.c	/^	Connection *connection;$/;"	m	struct:ConnectionStack_st	file:
connectionMemory	scaffold.c	/^static RecycleBin *connectionMemory = NULL;$/;"	v	file:
connectionSingleRotateWithLeft	scaffold.c	/^static Connection *connectionSingleRotateWithLeft(Connection * K2)$/;"	f	file:
connectionSingleRotateWithRight	scaffold.c	/^static Connection *connectionSingleRotateWithRight(Connection * K1)$/;"	f	file:
connectionStackMemory	scaffold.c	/^RecycleBin *connectionStackMemory = NULL;$/;"	v
connection_st	scaffold.c	/^struct connection_st {$/;"	s	file:
conserveVariant	correctedGraph.c	/^static boolean conserveVariant = false;$/;"	v	file:
convertInsertionMarkers	preGraphConstruction.c	/^static void convertInsertionMarkers(InsertionMarker * insertionMarkers,$/;"	f	file:
convertMarker	preGraphConstruction.c	/^static void convertMarker(InsertionMarker * marker, IDnum nodeID)$/;"	f	file:
convertSequences	readSet.c	/^void convertSequences(ReadSet * rs)$/;"	f
coord	roadMap.c	/^	ShortLength 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)$/;"	f	file:
copyPassageMarkerList	passageMarker.c	/^PassageMarkerList *copyPassageMarkerList(PassageMarkerList * list)$/;"	f
copyPreMarker	preGraph.c	/^static void copyPreMarker(PreMarker * dest, PreMarker * source, IDnum preNodeAID, PreGraph * preGraph) {$/;"	f	file:
correctGraph	correctedGraph.c	/^void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category * argSequenceCategories, boolean conserveLong, FILE * variantsF, double cov_cutoff_arg)$/;"	f
correctGraphLocally	locallyCorrectedGraph.c	/^void correctGraphLocally(Node * argStart)$/;"	f
countCoOccurences	scaffold.c	/^static unsigned char * countCoOccurences(IDnum * coOccurencesCount,$/;"	f	file:
countLocalBreakpoints	graphStats.c	/^int countLocalBreakpoints(PassageMarkerI marker, IDnum firstStrain)$/;"	f
countMappings	graphReConstruction.c	/^static IDnum countMappings(char * preGraphFilename) {$/;"	f	file:
countPreNodes	preGraphConstruction.c	/^countPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;"	f	file:
countReferenceKmers	splayTable.c	/^static Coordinate countReferenceKmers(ReadSet * reads, int wordLength) {$/;"	f	file:
countShortReads	scaffold.c	/^static IDnum **countShortReads(Graph * graph, ReadSet * reads)$/;"	f	file:
countVariantMarkers	graphStats.c	/^static IDnum countVariantMarkers(Node * node, IDnum sequenceCount) {$/;"	f	file:
counter	readSet.c	/^	IDnum counter;$/;"	m	struct:referenceCoordinate_st	file:
cov_cutoff	correctedGraph.c	/^static double cov_cutoff = -1;$/;"	v	file:
createAnalogousArc	graph.c	/^void createAnalogousArc(Node * originNode, Node * destinationNode,$/;"	f
createAnalogousPreArc_pg	preGraph.c	/^void createAnalogousPreArc_pg(IDnum originPreNodeID,$/;"	f
createArc	graph.c	/^Arc *createArc(Node * originNode, Node * destinationNode, Graph * graph)$/;"	f
createBinary	readSet.c	/^boolean createBinary = false;$/;"	v
createConnection	scaffold.c	/^static void createConnection(IDnum nodeID,$/;"	f	file:
createNewConnection	scaffold.c	/^Connection *createNewConnection(IDnum nodeID, IDnum node2ID,$/;"	f
createNodeLocks	graphReConstruction.c	/^createNodeLocks(Graph *graph)$/;"	f	file:
createNodeLocks	preGraphConstruction.c	/^static void createNodeLocks(PreGraph *preGraph)$/;"	f	file:
createNodeLocks	scaffold.c	/^createNodeLocks(Graph *graph)$/;"	f	file:
createNodeReadStartArrays	graph.c	/^void createNodeReadStartArrays(Graph * graph)$/;"	f
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
createReadsLocks	scaffold.c	/^createReadsLocks()$/;"	f	file:
createTwinConnection	scaffold.c	/^static void createTwinConnection(IDnum nodeID, IDnum node2ID,$/;"	f	file:
createTwinConnectionInTree	scaffold.c	/^static void createTwinConnectionInTree(IDnum nodeID,$/;"	f	file:
createVariantList	graphStats.c	/^static Variant * createVariantList(Node * node, Graph * graph) {$/;"	f	file:
currentBlocks	allocArray.h	/^	size_t currentBlocks;$/;"	m	struct:AllocArray_st
currentElements	allocArray.h	/^	size_t currentElements;$/;"	m	struct:AllocArray_st
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:
deallocateConnectionStack	scaffold.c	/^static void deallocateConnectionStack(ConnectionStack *stack)$/;"	f	file:
deallocateDFibHeapNode	dfib.c	/^static void deallocateDFibHeapNode(DFibHeapNode * a, DFibHeap * heap)$/;"	f	file:
deallocateFibHeapEl	fib.c	/^static void deallocateFibHeapEl(FibHeapNode * a, FibHeap * heap)$/;"	f	file:
deallocateMask	graphStats.c	/^static void deallocateMask(Mask * mask)$/;"	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:
debug	splayTable.c	/^boolean debug = false;$/;"	v
deleteNextPassageMarker	passageMarker.c	/^void deleteNextPassageMarker(PassageMarkerI marker, Graph * graph)$/;"	f
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)$/;"	f
destroyAllocArrayArray	allocArray.c	/^void destroyAllocArrayArray(AllocArray *allocArray)$/;"	f
destroyAllocArrayChunks	allocArray.c	/^destroyAllocArrayChunks (AllocArray *array)$/;"	f
destroyAnnotationBuffers	splayTable.c	/^static void destroyAnnotationBuffers(void)$/;"	f	file:
destroyArc	graph.c	/^void destroyArc(Arc * arc, Graph * graph)$/;"	f
destroyConnection	scaffold.c	/^void destroyConnection(Connection * connect, IDnum nodeID)$/;"	f
destroyConnectionStackMemory	scaffold.c	/^static void destroyConnectionStackMemory(void)$/;"	f	file:
destroyDHeap	dfibHeap.c	/^void destroyDHeap(DFibHeap * heap)$/;"	f
destroyFormattedWriter	utility.c	/^void destroyFormattedWriter(FormattedWriter * writer) {$/;"	f
destroyGraph	graph.c	/^void destroyGraph(Graph * graph)$/;"	f
destroyHeap	fibHeap.c	/^void destroyHeap(FibHeap * heap)$/;"	f
destroyKmerOccurenceTable	kmerOccurenceTable.c	/^void destroyKmerOccurenceTable(KmerOccurenceTable * kmerTable) {$/;"	f
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:
destroyNodePassageMarkers	graphStats.c	/^destroyNodePassageMarkers(Graph *graph,$/;"	f	file:
destroyPassageMarker	passageMarker.c	/^void destroyPassageMarker(PassageMarkerI marker)$/;"	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)$/;"	f
destroyReadSet	readSet.c	/^void destroyReadSet(ReadSet * reads)$/;"	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) {$/;"	f
destroySmallNodeListMemmory	graphReConstruction.c	/^static void destroySmallNodeListMemmory(void)$/;"	f	file:
destroySplayTable	splayTable.c	/^void destroySplayTable(SplayTable * splayTable)$/;"	f
destroyStringBuffer	utility.c	/^void destroyStringBuffer(StringBuffer *buffer, boolean freeString)$/;"	f
destroyTightString	tightString.c	/^void destroyTightString(TightString * tString)$/;"	f
detachDubiousReads	readSet.c	/^void detachDubiousReads(ReadSet * reads, boolean * dubiousReads)$/;"	f
determineEligibleStartingPoints	correctedGraph.c	/^static void determineEligibleStartingPoints()$/;"	f	file:
dfh_Dl	dfibpriv.h	/^	IDnum dfh_Dl;$/;"	m	struct:dfibheap
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_cons	dfibpriv.h	/^	DFibHeapNode **dfh_cons;$/;"	m	struct:dfibheap
dfh_consolidate	dfib.c	/^static void dfh_consolidate(DFibHeap * h)$/;"	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_min	dfibpriv.h	/^	DFibHeapNode *dfh_min;$/;"	m	struct:dfibheap
dfh_n	dfibpriv.h	/^	IDnum dfh_n;$/;"	m	struct:dfibheap
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
dfh_root	dfibpriv.h	/^	DFibHeapNode *dfh_root;$/;"	m	struct:dfibheap
dfhe_child	dfibpriv.h	/^	DFibHeapNode *dfhe_child;$/;"	m	struct:dfibheap_el
dfhe_data	dfibpriv.h	/^	void *dfhe_data;$/;"	m	struct:dfibheap_el
dfhe_degree	dfibpriv.h	/^	int dfhe_degree;$/;"	m	struct:dfibheap_el
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_key	dfibpriv.h	/^	Time dfhe_key;$/;"	m	struct:dfibheap_el
dfhe_left	dfibpriv.h	/^	DFibHeapNode *dfhe_left;$/;"	m	struct:dfibheap_el
dfhe_mark	dfibpriv.h	/^	boolean dfhe_mark;$/;"	m	struct:dfibheap_el
dfhe_newelem	dfib.c	/^static DFibHeapNode *dfhe_newelem(DFibHeap * h)$/;"	f	file:
dfhe_p	dfibpriv.h	/^	DFibHeapNode *dfhe_p;$/;"	m	struct:dfibheap_el
dfhe_remove	dfib.c	/^static DFibHeapNode *dfhe_remove(DFibHeapNode * x)$/;"	f	file:
dfhe_right	dfibpriv.h	/^	DFibHeapNode *dfhe_right;$/;"	m	struct:dfibheap_el
dfibheap	dfibpriv.h	/^struct dfibheap {$/;"	s
dfibheap_el	dfibpriv.h	/^struct dfibheap_el {$/;"	s
dfibheap_el_getKey	dfib.c	/^Time dfibheap_el_getKey(DFibHeapNode * node)$/;"	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;$/;"	v	file:
directVariantSequence	graphStats.c	/^static char * directVariantSequence(TightString * tString, Variant * variant, Graph * graph) {$/;"	f	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)$/;"	f
displayGeneralStatistics	graphStats.c	/^void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads)$/;"	f
displayLocalBreakpoint	graphStats.c	/^void displayLocalBreakpoint(PassageMarkerI strainMarker,$/;"	f
distance	scaffold.c	/^	float distance;$/;"	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;$/;"	m	struct:preGraph_st	file:
double_strand	roadMap.h	/^	boolean double_strand;$/;"	m	struct:roadMapArray_st
double_strand	splayTable.c	/^	boolean double_strand;$/;"	m	struct:splayTable_st	file:
double_stranded	graph.c	/^	boolean double_stranded;$/;"	m	struct:graph_st	file:
elementSize	allocArray.h	/^	size_t elementSize;$/;"	m	struct:AllocArray_st
elementsAllocated	allocArray.h	/^	size_t elementsAllocated;$/;"	m	struct:AllocArray_st
elementsRecycled	allocArray.h	/^	size_t elementsRecycled;$/;"	m	struct:AllocArray_st
eligibleStartingPoints	correctedGraph.c	/^static IDnum *eligibleStartingPoints;$/;"	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)$/;"	f
estimateLibraryInsertLength	scaffold.c	/^static void estimateLibraryInsertLength(IDnum * coOccurences, IDnum coOccurencesCount, Category libID) {$/;"	f	file:
estimateLibraryInsertLengths	scaffold.c	/^static void estimateLibraryInsertLengths(IDnum ** 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,$/;"	f
expectedNumberOfConnections	scaffold.c	/^static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,$/;"	f	file:
expected_coverage	readCoherentGraph.c	/^static double expected_coverage = 1;$/;"	v	file:
exploitShortReadPairs	shortReadPairs.c	/^void exploitShortReadPairs(Graph * argGraph,$/;"	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
exportGraph	graph.c	/^void exportGraph(char *filename, Graph * graph, TightString * sequences)$/;"	f
exportLongNodeMapping	graphStats.c	/^static void exportLongNodeMapping(FILE * outfile, Node * node, ReadSet * reads, ReferenceCoord * refCoords, int wordLength) {$/;"	f	file:
exportLongNodeMappings	graphStats.c	/^void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,$/;"	f
exportLongNodeSequence	graphStats.c	/^static void exportLongNodeSequence(FormattedWriter * writer, Node * node, Graph * graph, ReadSet * reads, ShortLength * readLengths, IDnum cutoff, ReadSet * variantSequences) {$/;"	f	file:
exportLongNodeSequences	graphStats.c	/^void exportLongNodeSequences(char *filename, char * variantsFilename, 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 refIndex, PreGraph * preGraph) {$/;"	f	file:
exportTightString	tightString.c	/^void exportTightString(FILE * outfile, TightString * sequence, IDnum index)$/;"	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:
extractVariantMarkers	graphStats.c	/^static void extractVariantMarkers(Variant * variants, Node * node, IDnum sequenceCount, int wordLength) {$/;"	f	file:
false	globals.h	30;"	d
fastPath	correctedGraph.c	/^static PassageMarkerI fastPath;$/;"	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_Dl	fibpriv.h	/^	IDnum fh_Dl;$/;"	m	struct:fibheap
fh_cascading_cut	fib.c	/^static void fh_cascading_cut(FibHeap * h, FibHeapNode * y)$/;"	f	file:
fh_checkcons	fib.c	/^static void fh_checkcons(FibHeap * h)$/;"	f	file:
fh_cmp_fnct	fibpriv.h	/^	Coordinate(*fh_cmp_fnct) (void *, void *);$/;"	m	struct:fibheap
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_cons	fibpriv.h	/^	FibHeapNode **fh_cons;$/;"	m	struct:fibheap
fh_consolidate	fib.c	/^static void fh_consolidate(FibHeap * h)$/;"	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_keys	fibpriv.h	/^	boolean fh_keys;$/;"	m	struct:fibheap
fh_makeheap	fib.c	/^FibHeap *fh_makeheap()$/;"	f
fh_makekeyheap	fib.c	/^FibHeap *fh_makekeyheap()$/;"	f
fh_min	fib.c	/^void *fh_min(FibHeap * h)$/;"	f
fh_min	fibpriv.h	/^	FibHeapNode *fh_min;$/;"	m	struct:fibheap
fh_minkey	fib.c	/^Coordinate fh_minkey(FibHeap * h)$/;"	f
fh_n	fibpriv.h	/^	IDnum fh_n;$/;"	m	struct:fibheap
fh_neginf	fibpriv.h	/^	void *fh_neginf;$/;"	m	struct:fibheap
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_root	fibpriv.h	/^	FibHeapNode *fh_root;$/;"	m	struct:fibheap
fh_setcmp	fib.c	/^voidcmp fh_setcmp(FibHeap * h, voidcmp fnct)$/;"	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_child	fibpriv.h	/^	FibHeapNode *fhe_child;$/;"	m	struct:fibheap_el
fhe_data	fibpriv.h	/^	void *fhe_data;$/;"	m	struct:fibheap_el
fhe_degree	fibpriv.h	/^	int fhe_degree;$/;"	m	struct:fibheap_el
fhe_initelem	fib.c	/^static void fhe_initelem(FibHeapNode * e)$/;"	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_key	fibpriv.h	/^	Coordinate fhe_key;$/;"	m	struct:fibheap_el
fhe_left	fibpriv.h	/^	FibHeapNode *fhe_left;$/;"	m	struct:fibheap_el
fhe_mark	fibpriv.h	/^	boolean fhe_mark;$/;"	m	struct:fibheap_el
fhe_newelem	fib.c	/^static FibHeapNode *fhe_newelem(FibHeap * h)$/;"	f	file:
fhe_p	fibpriv.h	/^	FibHeapNode *fhe_p;$/;"	m	struct:fibheap_el
fhe_remove	fib.c	/^static FibHeapNode *fhe_remove(FibHeapNode * x)$/;"	f	file:
fhe_right	fibpriv.h	/^	FibHeapNode *fhe_right;$/;"	m	struct:fibheap_el
fibheap	fibpriv.h	/^struct fibheap {$/;"	s
fibheap_el	fibpriv.h	/^struct fibheap_el {$/;"	s
fillNewConnectionInTree	scaffold.c	/^static void fillNewConnectionInTree(Connection *connect,$/;"	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:
fillUpConnectedGraph	graphReConstruction.c	/^static void fillUpConnectedGraph(ReadSet * reads,$/;"	f	file:
fillUpGraph	graphReConstruction.c	/^static void fillUpGraph(ReadSet * reads,$/;"	f	file:
findConnection	scaffold.c	/^static Connection* findConnection(IDnum nodeID,$/;"	f	file:
findIDnumInArray	graph.c	/^boolean findIDnumInArray(IDnum query, IDnum * array, IDnum arrayLength)$/;"	f
findInTree	splay.c	/^Kmer * findInTree(Kmer * X, SplayTree ** T)$/;"	f
findKmerInKmerOccurenceTable	kmerOccurenceTable.c	/^KmerOccurence *findKmerInKmerOccurenceTable(Kmer * kmer,$/;"	f
findLowCoverageRegions	graphStats.c	/^static Mask * findLowCoverageRegions(Node * node, Graph * graph, IDnum cutoff, ReadSet * reads, ShortLength * readLengths) {$/;"	f	file:
findOppositeNode	shortReadPairs.c	/^static void findOppositeNode(Node * node, Node ** oppositeNode,$/;"	f	file:
findOrCreateConnection	scaffold.c	/^static Connection* findOrCreateConnection(IDnum nodeID,$/;"	f	file:
findOrInsertOccurenceInSplayTable	splayTable.c	/^static boolean findOrInsertOccurenceInSplayTable(Kmer * kmer, IDnum * seqID,$/;"	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	/^	Coordinate finish;$/;"	m	struct:variant_st	file:
finish	graphStats.c	/^	IDnum finish;$/;"	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	readSet.h	/^	Coordinate finish;$/;"	m	struct:mask_st
finish	roadMap.c	/^	union positionPtr finish;	\/\/ 32$/;"	m	struct:annotation_st	typeref:union:annotation_st::positionPtr	file:
finishOffset	passageMarker.c	/^	IDnum finishOffset;$/;"	m	struct:passage_st	file:
flushFormattedWriter	utility.c	/^static void flushFormattedWriter(FormattedWriter * writer) {$/;"	f	file:
foldSymmetricalNode	correctedGraph.c	/^static void foldSymmetricalNode(Node * node)$/;"	f	file:
foldSymmetricalNodeReads	graph.c	/^void foldSymmetricalNodeReads(Node * node, Graph * graph)$/;"	f
formattedWriter_st	utility.h	/^typedef struct formattedWriter_st {$/;"	s
freeDoneTickets	correctedGraph.c	/^static void freeDoneTickets()$/;"	f	file:
freeElements	allocArray.h	/^	AllocArrayFreeElement *freeElements;$/;"	m	struct:AllocArray_st
frontReference	shortReadPairs.c	/^	Connection *frontReference;$/;"	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
getAnnotationInArray	roadMap.c	/^Annotation *getAnnotationInArray(Annotation * annot, Coordinate index)$/;"	f
getAnnotationLength	roadMap.c	/^Coordinate getAnnotationLength(Annotation * annot)$/;"	f
getArc	graph.c	/^Arc *getArc(Node * node)$/;"	f
getArcBetweenNodes	graph.c	/^Arc *getArcBetweenNodes(Node * originNode, Node * destinationNode,$/;"	f
getCnySeqNucl	binarySequences.c	/^void getCnySeqNucl(SequencesReader *seqReadInfo, uint8_t *sequence) {$/;"	f
getConnection	scaffold.c	/^Connection * getConnection(Node * node) {$/;"	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) {$/;"	f
getDestination	graph.c	/^Node *getDestination(Arc * arc)$/;"	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
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)$/;"	f
getLongCoverage	graphStats.c	/^static Coordinate getLongCoverage(Node * node) {$/;"	f	file:
getLongReadCoords	graphStats.c	/^static void getLongReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ReadSet * reads, IDnum offset) {$/;"	f	file:
getMarkedNodeList	shortReadPairs.c	/^NodeList *getMarkedNodeList()$/;"	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)$/;"	f
getNucleotideInDescriptor	graph.c	/^static Nucleotide getNucleotideInDescriptor(Descriptor * descriptor,$/;"	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
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)$/;"	f
getSequenceLengths	readSet.c	/^ShortLength *getSequenceLengths(ReadSet * reads, int wordLength)$/;"	f
getShortReadCoords	graphStats.c	/^static void getShortReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths) {$/;"	f	file:
getShortReadMarkerAtIndex	graph.c	/^ShortReadMarker *getShortReadMarkerAtIndex(ShortReadMarker * array,$/;"	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)$/;"	f
getShortReadTwinCoords	graphStats.c	/^static void getShortReadTwinCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths, IDnum offset) {$/;"	f	file:
getStart	roadMap.c	/^Coordinate getStart(Annotation * annot)$/;"	f
getStartID	roadMap.c	/^IDnum getStartID(Annotation * annot)$/;"	f
getStartOffset	passageMarker.c	/^Coordinate getStartOffset(PassageMarkerI marker)$/;"	f
getTail	correctedGraph.c	/^static PassageMarkerI getTail(PassageMarkerI marker) {$/;"	f	file:
getTightStringInArray	tightString.c	/^TightString *getTightStringInArray(TightString * tString,$/;"	f
getTipLength	correctedGraph.c	/^static Coordinate getTipLength(Node * node)$/;"	f	file:
getTotalCoverage	graph.c	/^Coordinate getTotalCoverage(Node * node)$/;"	f
getTwinConnection	scaffold.c	/^Connection * getTwinConnection(Connection * connect) {$/;"	f
getTwinMarker	passageMarker.c	/^PassageMarkerI getTwinMarker(PassageMarkerI marker)$/;"	f
getTwinNode	graph.c	/^Node *getTwinNode(Node * node)$/;"	f
getUniqueness	graph.c	/^boolean getUniqueness(Node * node)$/;"	f
getVirtualCoverage	graph.c	/^Coordinate getVirtualCoverage(Node * node)$/;"	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 {$/;"	s	file:
handicapNode	shortReadPairs.c	/^void handicapNode(Node * node)$/;"	f
hasPreMarkers	preGraph.c	/^boolean hasPreMarkers(IDnum nodeID, PreGraph * preGraph) {$/;"	f
hasReferenceMarker	graphStats.c	/^static boolean hasReferenceMarker(Node * node, ReadSet * reads) {$/;"	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:
identifyUniqueNodes	readCoherentGraph.c	/^static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))$/;"	f	file:
idx	allocArray.c	/^	ArrayIdx idx;$/;"	m	struct:AllocArrayFreeElement_st	file:
importCnyReadSet	binarySequences.c	/^ReadSet *importCnyReadSet(char *filename)$/;"	f
importConnectedGraph	graphReConstruction.c	/^Graph *importConnectedGraph(char *connectedGraphFilename, ReadSet * reads, char * roadmapFilename,$/;"	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
importReferenceRoadMapArray	roadMap.c	/^RoadMapArray *importReferenceRoadMapArray(char *filename)$/;"	f
importRoadMapArray	roadMap.c	/^RoadMapArray *importRoadMapArray(char *filename)$/;"	f
importSequences	readSet.c	/^ReadSet *importSequences(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,$/;"	f
incrementVirtualCoverage	graph.c	/^void incrementVirtualCoverage(Node * node,$/;"	f
indirectVariantSequence	graphStats.c	/^static char * indirectVariantSequence(TightString * tString, Variant * variant, Graph * graph) {$/;"	f	file:
initAllocArray	allocArray.c	/^static void initAllocArray(AllocArray * array, size_t elementSize, char * name) $/;"	f	file:
initAllocArrayArray	allocArray.c	/^static void initAllocArrayArray(AllocArray *array,$/;"	f	file:
initAnnotationBuffers	splayTable.c	/^static void initAnnotationBuffers(void)$/;"	f	file:
initConnectionStackMemory	scaffold.c	/^static void initConnectionStackMemory(void)$/;"	f	file:
initRecycleBin	recycleBin.c	/^static void initRecycleBin(RecycleBin *recycleBin,$/;"	f	file:
initSmallNodeListMemory	graphReConstruction.c	/^static void initSmallNodeListMemory(void)$/;"	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
inline	globals.h	53;"	d
input	utility.h	/^	FILE * input;$/;"	m	struct:formattedWriter_st
inputCnySeqFileStart	binarySequences.c	/^void inputCnySeqFileStart(Category category, SequencesWriter *seqWriteInfo)$/;"	f
inputReferenceIntoSplayTable	splayTable.c	/^void inputReferenceIntoSplayTable(TightString * tString,$/;"	f
inputSequenceArrayIntoSplayTableAndArchive	splayTable.c	/^void inputSequenceArrayIntoSplayTableAndArchive(ReadSet * reads,$/;"	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:
ints	kmer.h	/^	uint16_t ints;$/;"	m	struct:kmer_st
isCreateBinary	readSet.c	/^inline boolean isCreateBinary()$/;"	f
isDestinationToMarker	passageMarker.c	/^boolean isDestinationToMarker(PassageMarkerI marker, Node * node)$/;"	f
isEligibleTip	concatenatedPreGraph.c	/^static boolean isEligibleTip(IDnum index, PreGraph * preGraph, Coordinate$/;"	f	file:
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)$/;"	f	file:
isLocallyInitial	concatenatedGraph.c	/^static boolean isLocallyInitial(PassageMarkerI marker) {$/;"	f	file:
isLoop_pg	preGraph.c	/^boolean isLoop_pg(PreArcI preArc)$/;"	f
isMixed	graphStats.c	/^boolean isMixed(Node * node, IDnum firstStrain)$/;"	f
isNodeMemorized	graphReConstruction.c	/^static inline boolean isNodeMemorized(Node * node, SmallNodeList * nodePile)$/;"	f	file:
isOnlyGenome	graphStats.c	/^boolean isOnlyGenome(Node * node, IDnum firstStrain)$/;"	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)$/;"	f
isUniqueSolexa	readCoherentGraph.c	/^boolean isUniqueSolexa(Node * node)$/;"	f
isVariantMarker	graphStats.c	/^static boolean isVariantMarker(PassageMarkerI marker, IDnum sequenceCount) {$/;"	f	file:
keyFilter	kmer.c	/^static uint64_t keyFilter = 0;$/;"	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:
kmerProbabilities	readSet.h	/^	Probability **kmerProbabilities;$/;"	m	struct:readSet_st
kmerTable	kmerOccurenceTable.c	/^	KmerOccurence *kmerTable;$/;"	m	struct:kmerOccurenceTable_st	file:
kmerTableSize	kmerOccurenceTable.c	/^	IDnum kmerTableSize;$/;"	m	struct:kmerOccurenceTable_st	file:
kmer_st	kmer.h	/^struct kmer_st {$/;"	s
labels	readSet.h	/^	char **labels;$/;"	m	struct:readSet_st
left	scaffold.c	/^	Connection *left;$/;"	m	struct:connection_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$/;"	m	struct:annotation_st	file:
length	roadMap.h	/^	IDnum length;$/;"	m	struct:roadMapArray_st
length	tightString.h	/^	IDnum length;$/;"	m	struct:tString_st
length	utility.h	/^	size_t length;$/;"	m	struct:__anon2
lineLength	utility.h	/^	size_t lineLength;$/;"	m	struct:formattedWriter_st
listMemory	passageMarker.c	/^static RecycleBin *listMemory = NULL;$/;"	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)$/;"	f	file:
lockNode	preGraphConstruction.c	/^static void lockNode(IDnum preNodeID)$/;"	f	file:
lockRead	scaffold.c	/^static inline void lockRead(IDnum readID)$/;"	f	file:
lockTwoNodes	graphReConstruction.c	/^static inline void lockTwoNodes(Node *node, Node *node2)$/;"	f	file:
lockTwoNodes	preGraphConstruction.c	/^static void lockTwoNodes(IDnum preNodeID, IDnum preNode2ID)$/;"	f	file:
lockTwoNodes	scaffold.c	/^static inline void lockTwoNodes(IDnum nodeID, IDnum node2ID)$/;"	f	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); $/;"	v	file:
longlongs	kmer.h	/^	uint64_t longlongs[KMER_LONGLONGS];$/;"	m	struct:kmer_st
longs	kmer.h	/^	uint32_t longs;$/;"	m	struct:kmer_st
lowCoverageRegions	graphStats.c	/^static Mask * lowCoverageRegions(Coordinate * starts, Coordinate * stops, size_t length, IDnum cutoff, Coordinate nodeLength) {$/;"	f	file:
m_bColor	binarySequences.h	/^	boolean		m_bColor;$/;"	m	struct:__anon1
m_bDoubleStrand	binarySequences.h	/^	boolean		m_bDoubleStrand;$/;"	m	struct:__anon1
m_bFileWriteCompleted	binarySequences.h	/^	boolean		m_bFileWriteCompleted;$/;"	m	struct:__anon1
m_bIsBinary	binarySequences.h	/^	boolean		m_bIsBinary;$/;"	m	struct:sequencesReader_st
m_bIsRef	binarySequences.h	/^	boolean         m_bIsRef;$/;"	m	struct:sequencesReader_st
m_bIsRef	binarySequences.h	/^	boolean         m_bIsRef;$/;"	m	struct:sequencesWriter_st
m_currCategory	binarySequences.h	/^	Category	m_currCategory;$/;"	m	struct:sequencesReader_st
m_current	binarySequences.h	/^	Mask *          m_current;$/;"	m	struct:sequencesWriter_st
m_currentNuclReadIdx	binarySequences.h	/^	uint64_t	m_currentNuclReadIdx;$/;"	m	struct:sequencesReader_st
m_currentReadLength	binarySequences.h	/^	uint64_t	m_currentReadLength;$/;"	m	struct:sequencesReader_st
m_elem	binarySequences.h	/^	RefInfo		m_elem;$/;"	m	struct:refInfoList_st
m_fileSegmentWriteIdx	binarySequences.h	/^	uint32_t	m_fileSegmentWriteIdx;$/;"	m	struct:sequencesWriter_st
m_hostBufferFilePos	binarySequences.h	/^	int64_t		m_hostBufferFilePos[3];$/;"	m	struct:sequencesWriter_st
m_hostBuffersInUse	binarySequences.h	/^	uint32_t	m_hostBuffersInUse;$/;"	m	struct:sequencesWriter_st
m_insertCurrentIndex	binarySequences.h	/^	uint64_t	m_insertCurrentIndex;$/;"	m	struct:sequencesWriter_st
m_insertLength	binarySequences.h	/^	uint64_t	m_insertLength;$/;"	m	struct:sequencesWriter_st
m_insertLengthIndex	binarySequences.h	/^	uint64_t	m_insertLengthIndex;$/;"	m	struct:sequencesWriter_st
m_insertStartIndex	binarySequences.h	/^	uint64_t	m_insertStartIndex;$/;"	m	struct:sequencesWriter_st
m_magic	binarySequences.h	/^	uint32_t	m_magic;$/;"	m	struct:__anon1
m_maskMemory	binarySequences.h	/^	RecycleBin *    m_maskMemory;$/;"	m	struct:sequencesWriter_st
m_maxSeqLen	binarySequences.h	/^	uint64_t	m_maxSeqLen;$/;"	m	struct:__anon1
m_maxSeqLen	binarySequences.h	/^	uint64_t	m_maxSeqLen;$/;"	m	struct:sequencesReader_st
m_minSeqLen	binarySequences.h	/^	uint64_t	m_minSeqLen;$/;"	m	struct:__anon1
m_minSeqLen	binarySequences.h	/^	uint64_t	m_minSeqLen;$/;"	m	struct:sequencesReader_st
m_nameFile	binarySequences.h	/^	FILE *          m_nameFile;$/;"	m	struct:sequencesWriter_st
m_namesFilename	binarySequences.h	/^	char *		m_namesFilename;$/;"	m	struct:sequencesReader_st
m_numCategories	binarySequences.h	/^	Category	m_numCategories;$/;"	m	struct:__anon1
m_numCategories	binarySequences.h	/^	Category	m_numCategories;$/;"	m	struct:sequencesReader_st
m_openMask	binarySequences.h	/^	boolean         m_openMask;$/;"	m	struct:sequencesWriter_st
m_pCurrentReadPtr	binarySequences.h	/^	uint8_t *	m_pCurrentReadPtr;$/;"	m	struct:sequencesReader_st
m_pFile	binarySequences.h	/^        FILE *		m_pFile;$/;"	m	struct:sequencesReader_st
m_pFile	binarySequences.h	/^        FILE *		m_pFile;$/;"	m	struct:sequencesWriter_st
m_pHostBufPtr	binarySequences.h	/^	uint8_t *	m_pHostBufPtr;$/;"	m	struct:sequencesWriter_st
m_pHostBufPtrMax	binarySequences.h	/^	uint8_t *	m_pHostBufPtrMax;$/;"	m	struct:sequencesWriter_st
m_pHostLengthBufPtr	binarySequences.h	/^	uint8_t *	m_pHostLengthBufPtr;$/;"	m	struct:sequencesWriter_st
m_pHostLengthBufPtrMax	binarySequences.h	/^	uint8_t *	m_pHostLengthBufPtrMax;$/;"	m	struct:sequencesWriter_st
m_pNextReadPtr	binarySequences.h	/^	uint8_t *	m_pNextReadPtr;$/;"	m	struct:sequencesReader_st
m_pReadBufEnd	binarySequences.h	/^	uint8_t *	m_pReadBufEnd;$/;"	m	struct:sequencesReader_st
m_pReadBuffer	binarySequences.h	/^	uint8_t *	m_pReadBuffer;$/;"	m	struct:sequencesReader_st
m_pWriteBuffer	binarySequences.h	/^	uint8_t	*	m_pWriteBuffer[3];$/;"	m	struct:sequencesWriter_st
m_pos	binarySequences.h	/^	int32_t         m_pos;$/;"	m	struct:refInfo_st
m_position	binarySequences.h	/^	Coordinate      m_position;$/;"	m	struct:sequencesWriter_st
m_ppCurrString	binarySequences.h	/^	char **		m_ppCurrString;$/;"	m	struct:sequencesReader_st
m_readBufPos	binarySequences.h	/^	uint64_t	m_readBufPos;$/;"	m	struct:sequencesReader_st
m_refCnt	binarySequences.h	/^	uint32_t        m_refCnt;$/;"	m	struct:sequencesReader_st
m_refCnt	binarySequences.h	/^	uint32_t        m_refCnt;$/;"	m	struct:sequencesWriter_st
m_refInfoHead	binarySequences.h	/^	RefInfoList *	m_refInfoHead;$/;"	m	struct:sequencesWriter_st
m_referenceID	binarySequences.h	/^	int32_t         m_referenceID;$/;"	m	struct:refInfo_st
m_referenceMask	binarySequences.h	/^	Mask **         m_referenceMask;$/;"	m	struct:sequencesWriter_st
m_seqFilename	binarySequences.h	/^	char *		m_seqFilename;$/;"	m	struct:sequencesReader_st
m_seqNuclStoreSize	binarySequences.h	/^	uint64_t	m_seqNuclStoreSize;$/;"	m	struct:__anon1
m_sequenceCnt	binarySequences.h	/^	uint64_t	m_sequenceCnt;$/;"	m	struct:__anon1
m_sequences	binarySequences.h	/^	ReadSet *       m_sequences;$/;"	m	struct:sequencesReader_st
m_timeStamp	binarySequences.h	/^	uint64_t	m_timeStamp;$/;"	m	struct:__anon1
m_totalSeqLen	binarySequences.h	/^	uint64_t	m_totalSeqLen;$/;"	m	struct:__anon1
m_unifiedSeqFileHeader	binarySequences.h	/^        CnyUnifiedSeqFileHeader m_unifiedSeqFileHeader;$/;"	m	struct:sequencesReader_st
m_unifiedSeqFileHeader	binarySequences.h	/^        CnyUnifiedSeqFileHeader m_unifiedSeqFileHeader;$/;"	m	struct:sequencesWriter_st
main	run.c	/^int main(int argc, char **argv)$/;"	f
main	run2.c	/^int main(int argc, char **argv)$/;"	f
mallocOrExit	utility.h	37;"	d
mallocOrExit3	utility.c	/^void *mallocOrExit3(size_t count, size_t size, const char *name)$/;"	f
mallocOrExitWithoutCast	utility.h	47;"	d
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$/;"	m	struct:node_st	file:
marker	graphStats.c	/^	PassageMarkerI marker;$/;"	m	struct:variant_st	file:
marker	passageMarker.h	/^	PassageMarkerI marker;$/;"	m	struct:passageList_st
marker	readCoherentGraph.c	/^	PassageMarkerI marker;$/;"	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;$/;"	v	file:
maskMemory	graphStats.c	/^static RecycleBin * maskMemory = NULL;$/;"	v	file:
maskMemory	splayTable.c	/^static RecycleBin * maskMemory = NULL;$/;"	v	file:
mask_st	readSet.h	/^struct mask_st {$/;"	s
mateReads	readSet.h	/^	IDnum *mateReads;$/;"	m	struct:readSet_st
max	correctedGraph.c	/^static Time max(Time A, Time B, Time C)$/;"	f	file:
max	locallyCorrectedGraph.c	/^static Time max(Time A, Time B, Time C)$/;"	f	file:
maxBlocks	allocArray.h	/^	size_t maxBlocks;$/;"	m	struct:AllocArray_st
maxElements	allocArray.h	/^	size_t maxElements;$/;"	m	struct:AllocArray_st
maxLength	graphStats.c	/^Coordinate maxLength(Graph * graph)$/;"	f
measureCoOccurences	scaffold.c	/^static void measureCoOccurences(IDnum ** coOccurences,$/;"	f	file:
memorizeNode	graphReConstruction.c	/^static inline void memorizeNode(Node * node, SmallNodeList ** nodePile)$/;"	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 {$/;"	s	file:
moveCnySeqNucleotides	binarySequences.c	/^static void moveCnySeqNucleotides(SequencesWriter *seqWriteInfo)$/;"	f	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)$/;"	f
name	allocArray.h	/^	char *name;$/;"	m	struct:AllocArray_st
name	graphStats.c	/^	char * name;$/;"	m	struct:referenceCoord_st	file:
name	readSet.c	/^	char * name;$/;"	m	struct:referenceCoordinate_st	file:
nbPush	splayTable.c	/^static int *nbPush = NULL;$/;"	v	file:
nbThreads	allocArray.h	/^	int nbThreads;$/;"	m	struct:AllocArray_st
newAllocArray	allocArray.c	/^newAllocArray (size_t elementSize, char *name)$/;"	f
newAllocArrayArray	allocArray.c	/^AllocArray *newAllocArrayArray(unsigned int n,$/;"	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, SequencesReader *seqReadInfo,$/;"	f	file:
newFibHeap	fibHeap.c	/^FibHeap *newFibHeap()$/;"	f
newFormattedWriter	utility.c	/^FormattedWriter * newFormattedWriter(FILE * file, size_t lineLength) {$/;"	f
newKmerOccurenceTable	kmerOccurenceTable.c	/^KmerOccurenceTable * newKmerOccurenceTable(short int accelerationBits, int wordLength) {$/;"	f
newMask	graphStats.c	/^static Mask * newMask(Coordinate position)$/;"	f	file:
newMask	readSet.c	/^static Mask * newMask(SequencesWriter *seqWriteInfo, Coordinate position)$/;"	f	file:
newMask	splayTable.c	/^static Mask * newMask(Coordinate position)$/;"	f	file:
newNegativeDescriptor	graph.c	/^static Descriptor *newNegativeDescriptor(IDnum sequenceID,$/;"	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, SequencesReader *seqReadInfo)$/;"	f
newReadCoverage	graphStats.c	/^Coordinate newReadCoverage(Node * node, IDnum firstStrain)$/;"	f
newReadSet	readSet.c	/^ReadSet *newReadSet()$/;"	f
newRecycleBin	recycleBin.c	/^RecycleBin *newRecycleBin(size_t node_size, int nodes_per_chunk)$/;"	f
newRecycleBinArray	recycleBin.c	/^RecycleBin *newRecycleBinArray(unsigned int n,$/;"	f
newReferenceCoordinateTable	readSet.c	/^static ReferenceCoordinateTable * newReferenceCoordinateTable() {$/;"	f	file:
newSplayTable	splayTable.c	/^SplayTable *newSplayTable(int WORDLENGTH, boolean double_strand)$/;"	f
newStringBuffer	utility.c	/^StringBuffer *newStringBuffer(size_t size)$/;"	f
newTicket	correctedGraph.c	/^static Ticket *newTicket()$/;"	f	file:
newTightString	tightString.c	/^TightString *newTightString(Coordinate length)$/;"	f
newTightStringArrayFromStringArray	tightString.c	/^TightString *newTightStringArrayFromStringArray(char **sequences,$/;"	f
next	allocArray.c	/^	AllocArrayFreeElement *next;$/;"	m	struct:AllocArrayFreeElement_st	file:
next	binarySequences.h	/^	struct refInfoList_st *next;$/;"	m	struct:refInfoList_st	typeref:struct:refInfoList_st::refInfoList_st
next	correctedGraph.c	/^	Ticket *next;$/;"	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;$/;"	m	struct:smallNodeList_st	file:
next	locallyCorrectedGraph.h	/^	NodeList *next;$/;"	m	struct:nodeList_st
next	passageMarker.h	/^	PassageMarkerList *next;$/;"	m	struct:passageList_st
next	preGraph.c	/^	PreMarker * next;$/;"	m	struct:preMarker_st	file:
next	readCoherentGraph.c	/^	RBConnection *next;$/;"	m	struct:rb_connection_st	file:
next	readSet.h	/^	Mask* next;$/;"	m	struct:mask_st
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	/^	ConnectionStack *next;$/;"	m	struct:ConnectionStack_st	file:
nextInLookupTable	graph.c	/^	Arc *nextInLookupTable;	\/\/ 64$/;"	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;$/;"	m	struct:smallNodeList_st	file:
node	locallyCorrectedGraph.h	/^	Node *node;$/;"	m	struct:nodeList_st
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;$/;"	v	file:
nodeList_st	locallyCorrectedGraph.h	/^struct nodeList_st {$/;"	s
nodeLocks	graphReConstruction.c	/^static omp_lock_t *nodeLocks = NULL;$/;"	v	file:
nodeLocks	preGraphConstruction.c	/^static omp_lock_t *nodeLocks = NULL;$/;"	v	file:
nodeLocks	scaffold.c	/^static omp_lock_t *nodeLocks = NULL;$/;"	v	file:
nodeMask_st	graphReConstruction.c	/^struct nodeMask_st {$/;"	s	file:
nodeMemory	dfibpriv.h	/^	RecycleBin *nodeMemory;$/;"	m	struct:dfibheap
nodeMemory	fibpriv.h	/^	RecycleBin *nodeMemory;$/;"	m	struct:fibheap
nodeMemory	graph.c	/^static RecycleBin *nodeMemory = NULL;$/;"	v	file:
nodeReadCounts	graph.c	/^	IDnum *nodeReadCounts;$/;"	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:
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	kmerOccurenceTable.c	/^	IDnum offset;$/;"	m	struct:kmerOccurence_st	file:
offset	scaffold.c	/^	IDnum offset;$/;"	m	struct:readOccurence_st	file:
openCnySeqForRead	binarySequences.c	/^FILE *openCnySeqForRead(const char *fileName, CnyUnifiedSeqFileHeader *seqFileHeader)$/;"	f
openCnySeqForWrite	binarySequences.c	/^SequencesWriter * openCnySeqForWrite(const char *unifiedSeqFileName)$/;"	f
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
output	utility.h	/^	FILE * output;$/;"	m	struct:formattedWriter_st
pairedCategories	readSet.c	/^int pairedCategories(ReadSet * reads)$/;"	f
paired_count	scaffold.c	/^	IDnum paired_count;$/;"	m	struct:connection_st	file:
paired_exp_fraction	scaffold.c	/^static double paired_exp_fraction = 0.1;$/;"	v	file:
parseDataAndReadFiles	readSet.c	/^void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand, boolean * noHash)$/;"	f
passageList_st	passageMarker.h	/^struct passageList_st {$/;"	s
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,$/;"	f	file:
popConnectionStack	scaffold.c	/^static Connection *popConnectionStack(ConnectionStack **stack)$/;"	f	file:
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;$/;"	v	file:
previous	locallyCorrectedGraph.h	/^	NodeList *previous;$/;"	m	struct:nodeList_st
previous	preGraph.c	/^	PreMarker * previous;$/;"	m	struct:preMarker_st	file:
previousInNode	passageMarker.c	/^	PassageMarkerI previousInNode;$/;"	m	struct:passage_st	file:
printAnnotations	splayTable.c	/^static void printAnnotations(IDnum *sequenceIDs, Coordinate * coords,$/;"	f	file:
printConnections	scaffold.c	/^void printConnections(ReadSet * reads, boolean * shadows)$/;"	f
printKmer	kmer.c	/^void printKmer(Kmer * kmer) {$/;"	f
printReferenceCoordinateTableStats	readSet.c	/^static void printReferenceCoordinateTableStats(ReferenceCoordinateTable * table) {$/;"	f	file:
printScaffold	scaffold.c	/^void printScaffold(Graph * argGraph,$/;"	f
printShortCounts	graphStats.c	/^static void printShortCounts(FILE * outfile, Node * node, Graph * graph, ReadSet * reads)$/;"	f	file:
printUsage	readSet.c	/^static void printUsage()$/;"	f	file:
printUsage	run.c	/^static void printUsage()$/;"	f	file:
printUsage	run2.c	/^static void printUsage()$/;"	f	file:
producing	splayTable.c	/^static boolean producing = 1;$/;"	v	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
pushBuffer	splayTable.c	/^static void pushBuffer(int thread)$/;"	f	file:
pushBufferCommit	splayTable.c	/^static void pushBufferCommit(int thread)$/;"	f	file:
pushConnectionStack	scaffold.c	/^static void pushConnectionStack(ConnectionStack **stack, Connection *connection)$/;"	f	file:
pushNeighbours	shortReadPairs.c	/^static boolean pushNeighbours(Node * node, Node * oppositeNode,$/;"	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,$/;"	f	file:
readBAMFile	readSet.c	/^static void readBAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readBAMint32	readSet.c	/^static int readBAMint32(gzFile file)$/;"	f	file:
readCigar	readSet.c	/^static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {$/;"	f	file:
readCnySeqUint32	binarySequences.c	/^uint32_t readCnySeqUint32(SequencesReader *seqReadInfo) $/;"	f
readCnySeqUint8	binarySequences.c	/^static int32_t readCnySeqUint8(SequencesReader *seqReadInfo)$/;"	f	file:
readCoherentGraph	readCoherentGraph.c	/^void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node),$/;"	f
readConnectedGraphFile	graph.c	/^Graph *readConnectedGraphFile(char *connectedGraphFilename, boolean * double_strand)$/;"	f
readCount	readSet.h	/^	IDnum readCount;$/;"	m	struct:readSet_st
readCoverage	graphStats.c	/^Coordinate readCoverage(Node * node)$/;"	f
readFastAFile	readSet.c	/^static void readFastAFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readFastAGZFile	readSet.c	/^static void readFastAGZFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readFastQFile	readSet.c	/^static void readFastQFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readFastQGZFile	readSet.c	/^static void readFastQGZFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex)$/;"	f	file:
readID	graph.c	/^	IDnum readID;$/;"	m	struct:shortReadMarker_st	file:
readNucleotide	tightString.c	/^char readNucleotide(Nucleotide nucleotide)$/;"	f
readOccurence_st	scaffold.c	/^struct readOccurence_st {$/;"	s	file:
readPassageMarker	passageMarker.c	/^char *readPassageMarker(PassageMarkerI marker)$/;"	f
readPreGraphFile	graph.c	/^Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand)$/;"	f
readRawFile	readSet.c	/^static void readRawFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex)$/;"	f	file:
readRawGZFile	readSet.c	/^static void readRawGZFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex)$/;"	f	file:
readSAMFile	readSet.c	/^static void readSAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;"	f	file:
readSet_st	readSet.h	/^struct readSet_st {$/;"	s
readStartsAreActivated	graph.c	/^boolean readStartsAreActivated(Graph * graph)$/;"	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,$/;"	f
readjustConnectionInTree	scaffold.c	/^static void readjustConnectionInTree(Connection *connect,$/;"	f	file:
readjustMiniConnection	shortReadPairs.c	/^static void readjustMiniConnection(Node * node,$/;"	f	file:
readsLocks	scaffold.c	/^static omp_lock_t *readsLocks = NULL;$/;"	v	file:
reallocOrExit	utility.h	41;"	d
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:
reallocOrExitWithoutCast	utility.h	51;"	d
reallocateNodeDescriptor	graph.c	/^void reallocateNodeDescriptor(Node * node, Coordinate length) {$/;"	f
recenterLocalScaffold	shortReadPairs.c	/^static void recenterLocalScaffold(Node * node, Coordinate oldLength)$/;"	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:
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;$/;"	m	struct:refMap_st	file:
refInfoList_st	binarySequences.h	/^struct refInfoList_st {$/;"	s
refInfo_st	binarySequences.h	/^struct refInfo_st {$/;"	s
refMap_st	graphStats.c	/^typedef struct refMap_st {$/;"	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:
referenceCount	roadMap.h	/^	IDnum referenceCount;$/;"	m	struct:roadMapArray_st
referenceGraphKmers	graphReConstruction.c	/^static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,$/;"	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) {$/;"	f
referenceSequence	graphStats.c	/^static char * referenceSequence(TightString * nodeSequence, Variant * variant, Graph * graph) {$/;"	f	file:
referenceStart	graphReConstruction.c	/^	IDnum referenceStart;$/;"	m	struct:referenceMapping_st	file:
referenceStart	preGraph.c	/^	IDnum referenceStart;$/;"	m	struct:preMarker_st	file:
reference_coordinate_double_strand	readSet.c	/^static Coordinate reference_coordinate_double_strand = true;$/;"	v	file:
refillCnySeqReadBuffer	binarySequences.c	/^static boolean refillCnySeqReadBuffer(SequencesReader *seqReadInfo) $/;"	f	file:
remapBackOfNodeArcsOntoNeighbour	correctedGraph.c	/^static void remapBackOfNodeArcsOntoNeighbour(Node * source, Node * target)$/;"	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)$/;"	f	file:
removeHighCoverageNodes	graphStats.c	/^void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, char *filename)$/;"	f
removeLowArcs	graphStats.c	/^void removeLowArcs(Graph * graph, double cutoff) {$/;"	f
removeLowArcsFromNode	graphStats.c	/^static void removeLowArcsFromNode(Node* node, Graph * graph, double cutoff) {$/;"	f	file:
removeLowCoverageNodesAndDenounceDubiousReads	graphStats.c	/^boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,$/;"	f
removeLowCoverageReferenceNodes	graphStats.c	/^void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLongCov, ReadSet * reads)$/;"	f
removeLowLongCoverageNodesAndDenounceDubiousReads	graphStats.c	/^void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,$/;"	f
removeNextNodeFromDHeap	dfibHeap.c	/^Node *removeNextNodeFromDHeap(DFibHeap * heap)$/;"	f
removeNextNodeFromHeap	fibHeap.c	/^struct node_st *removeNextNodeFromHeap(FibHeap * heap)$/;"	f
removeNodeAndDenounceDubiousReads	graphStats.c	/^removeNodeAndDenounceDubiousReads(Graph *graph,$/;"	f	file:
removePreArcFromList_pg	preGraph.c	/^void removePreArcFromList_pg(PreArcI preArc, IDnum preNodeID,$/;"	f
removeStrainMarkers	graphStats.c	/^void removeStrainMarkers(Node * node, IDnum firstStrain)$/;"	f
removeUnreliableConnections	scaffold.c	/^static void removeUnreliableConnections(ReadSet * reads, boolean *shadows)$/;"	f	file:
renumberNodes	graph.c	/^void renumberNodes(Graph * graph)$/;"	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
resetCnySeqCurrentRead	binarySequences.c	/^void resetCnySeqCurrentRead(SequencesReader *seqReadInfo) $/;"	f
resetKeyFilter	kmer.c	/^void resetKeyFilter(int keyLength) {$/;"	f
resetMiniConnection	shortReadPairs.c	/^static void resetMiniConnection(Node * node, MiniConnection * localConnect,$/;"	f	file:
resetNodeStatus	graph.c	/^void resetNodeStatus(Graph * graph)$/;"	f
resetStringBuffer	utility.c	/^void resetStringBuffer(StringBuffer *buffer)$/;"	f
resetWordFilter	kmer.c	/^void resetWordFilter(int wordLength) {$/;"	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) {$/;"	f
right	scaffold.c	/^	Connection *right;$/;"	m	struct:connection_st	file:
right	splay.c	/^	struct splayNode_st *right;$/;"	m	struct:splayNode_st	typeref:struct:splayNode_st::splayNode_st	file:
roadMapArray_st	roadMap.h	/^struct roadMapArray_st {$/;"	s
roadmap_st	roadMap.c	/^struct roadmap_st {$/;"	s	file:
scaffold	scaffold.c	/^static Connection **scaffold = NULL;$/;"	v	file:
scanBinaryReferenceSequences	splayTable.c	/^Mask ** scanBinaryReferenceSequences(SequencesReader *seqReadInfo, IDnum referenceSequenceCount) {$/;"	f
scanReferenceSequences	splayTable.c	/^Mask ** scanReferenceSequences(FILE * file, IDnum referenceSequenceCount) {$/;"	f
secondInPair	readSet.h	/^	unsigned char *secondInPair;$/;"	m	struct:readSet_st
seqID	splay.c	/^	IDnum seqID;$/;"	m	struct:splayNode_st	file:
sequence	tightString.h	/^	Codon *sequence;$/;"	m	struct:tString_st
sequenceCategories	correctedGraph.c	/^static Category *sequenceCategories;$/;"	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 ShortLength *sequenceLengths;$/;"	v	file:
sequences	readCoherentGraph.c	/^static TightString *sequences = NULL;$/;"	v	file:
sequences	readSet.h	/^	char **sequences;$/;"	m	struct:readSet_st
sequencesReader_st	binarySequences.h	/^struct sequencesReader_st {$/;"	s
sequencesWriter_st	binarySequences.h	/^struct sequencesWriter_st {$/;"	s
setAllConnectionsClean	scaffold.c	/^static void setAllConnectionsClean(void)$/;"	f	file:
setCreateBinary	readSet.c	/^void setCreateBinary(boolean val)$/;"	f
setEmptyMiniConnection	shortReadPairs.c	/^static void setEmptyMiniConnection(Node * node)$/;"	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,$/;"	f
setPairedExpFraction	scaffold.c	/^void setPairedExpFraction(double x) {$/;"	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
setVirtualCoverage	graph.c	/^void setVirtualCoverage(Node * node,$/;"	f
shareReadStarts	graph.c	/^void shareReadStarts(Node * target, Node * source, Graph * graph)$/;"	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)$/;"	f	file:
slowPath	correctedGraph.c	/^static PassageMarkerI slowPath;$/;"	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:
sortCoords	graphStats.c	/^static void sortCoords(Coordinate * array, IDnum length) {$/;"	f	file:
sortGapMarkers	graph.c	/^void sortGapMarkers(Graph * graph)$/;"	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:
splayConnection	scaffold.c	/^static Connection *splayConnection(Connection * T, IDnum nodeID)$/;"	f	file:
splayNode_st	splay.c	/^struct splayNode_st {$/;"	s	file:
splayTable_st	splayTable.c	/^struct splayTable_st {$/;"	s	file:
splayToList	scaffold.c	/^static void splayToList(Connection **connection)$/;"	f	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;$/;"	m	struct:nodeMask_st	file:
start	graphStats.c	/^	Coordinate start;$/;"	m	struct:variant_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;$/;"	m	struct:referenceCoordinate_st	file:
start	readSet.h	/^	Coordinate start;$/;"	m	struct:mask_st
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;		\/\/ 1$/;"	m	struct:node_st	file:
status	passageMarker.c	/^	boolean status;$/;"	m	struct:passage_st	file:
str	utility.h	/^	char *str;$/;"	m	struct:__anon2
sufficientVariantCoverage	correctedGraph.c	/^static boolean sufficientVariantCoverage() {$/;"	f	file:
swap	dfib.c	73;"	d	file:
swap	fib.c	69;"	d	file:
tSeqMem	readSet.h	/^	char *tSeqMem;$/;"	m	struct:readSet_st
tSequences	readSet.h	/^	TightString *tSequences;$/;"	m	struct:readSet_st
tString_st	tightString.h	/^struct tString_st {$/;"	s
table	splayTable.c	/^	SplayTree **table;$/;"	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:
testConnection	scaffold.c	/^static boolean testConnection(IDnum IDA,$/;"	f	file:
threadSequenceThroughGraph	graphReConstruction.c	/^static void threadSequenceThroughGraph(TightString * tString,$/;"	f	file:
ticketMemory	correctedGraph.c	/^static RecycleBin *ticketMemory;$/;"	v	file:
timersub	utility.h	107;"	d
times	correctedGraph.c	/^static Time *times;$/;"	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)$/;"	f
tourBus	correctedGraph.c	/^static void tourBus(Node * startingPoint)$/;"	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:
trim3primeSlowPath	correctedGraph.c	/^static void trim3primeSlowPath(Coordinate seqLength) {$/;"	f	file:
trim5primeSlowPath	correctedGraph.c	/^static void trim5primeSlowPath() {$/;"	f	file:
trimLongReadTips	readCoherentGraph.c	/^static void trimLongReadTips()$/;"	f	file:
trimSlowPath	correctedGraph.c	/^static void trimSlowPath(Coordinate seqLength) {$/;"	f	file:
true	globals.h	29;"	d
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)$/;"	f	file:
unLockNode	preGraphConstruction.c	/^static void unLockNode(IDnum preNodeID)$/;"	f	file:
unLockRead	scaffold.c	/^static inline void unLockRead(IDnum readID)$/;"	f	file:
unLockTwoNodes	graphReConstruction.c	/^static inline void unLockTwoNodes(Node *node, Node *node2)$/;"	f	file:
unLockTwoNodes	preGraphConstruction.c	/^static void unLockTwoNodes(IDnum preNodeID, IDnum preNode2ID)$/;"	f	file:
unLockTwoNodes	scaffold.c	/^static inline void unLockTwoNodes(IDnum nodeID, IDnum node2ID)$/;"	f	file:
unMemorizeNodes	graphReConstruction.c	/^static void unMemorizeNodes(SmallNodeList ** nodePile)$/;"	f	file:
uniqueNodesConnect	readCoherentGraph.c	/^static boolean uniqueNodesConnect(Node * startingNode)$/;"	f	file:
uniqueness	graph.c	/^	boolean uniqueness;	\/\/ 1$/;"	m	struct:node_st	file:
unmarkInterestingNodes	shortReadPairs.c	/^static void unmarkInterestingNodes()$/;"	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) $/;"	f
variance	scaffold.c	/^	float variance;$/;"	m	struct:connection_st	file:
variance	shortReadPairs.c	/^	float variance;$/;"	m	struct:miniConnection_st	file:
variantCount	correctedGraph.c	/^static IDnum variantCount = 1;$/;"	v	file:
variantLength	graphStats.c	/^static Coordinate variantLength(Variant * variant) {$/;"	f	file:
variantSequence	graphStats.c	/^static char * variantSequence(ReadSet * variantSequences, Variant * variant, Graph * graph) {$/;"	f	file:
variant_st	graphStats.c	/^typedef struct variant_st {$/;"	s	file:
variantsFile	correctedGraph.c	/^static FILE * variantsFile = NULL;$/;"	v	file:
velvetFprintf	utility.c	/^void velvetFprintf(FILE * file, const char * format, ...) $/;"	f
velvetFprintfReferenceMapping	graphStats.c	/^static void velvetFprintfReferenceMapping(FILE * file, ReferenceMapping * mapping, ReferenceCoord * refCoords, int wordLength) {$/;"	f	file:
velvetLog	utility.c	/^void velvetLog(const char *format, ...)$/;"	f
velvetifySequence	readSet.c	/^static void velvetifySequence(char * str, SequencesWriter *seqWriteInfo) {$/;"	f	file:
virtualCoverage	graph.c	/^	IDnum virtualCoverage;	\/\/ 32 * 2$/;"	m	struct:node_st	file:
virtualCoverage	graph.c	/^	IDnum virtualCoverage[CATEGORIES];	\/\/ 32 * 2$/;"	m	struct:node_st	file:
voidcmp	fib.h	/^typedef Coordinate(*voidcmp) (void *, void *);$/;"	t
wordLength	graph.c	/^	int wordLength;$/;"	m	struct:graph_st	file:
wordLength	preGraph.c	/^	int wordLength;$/;"	m	struct:preGraph_st	file:
writeBuffers	splayTable.c	/^static void writeBuffers(FILE *outFile, int nbThreads)$/;"	f	file:
writeCharToFormattedWriter	utility.c	/^static void writeCharToFormattedWriter(FormattedWriter * writer, char c) {$/;"	f	file:
writeCnySeqNucleotide	binarySequences.c	/^static void writeCnySeqNucleotide(uint8_t nucleotide, SequencesWriter *seqWriteInfo)$/;"	f	file:
writeCnySeqUint32	binarySequences.c	/^static void writeCnySeqUint32(uint32_t uint32, SequencesWriter *seqWriteInfo)$/;"	f	file:
writeCnySeqUint8	binarySequences.c	/^static void writeCnySeqUint8(uint8_t uint8, SequencesWriter *seqWriteInfo)$/;"	f	file:
writeFastaSequence	readSet.c	/^static void writeFastaSequence(FILE * outfile, const char * str)$/;"	f	file:
writeMappedSequence	readSet.c	/^static void writeMappedSequence(IDnum * sequenceIndex, Category cat, Category prev_cat, char * previous_seq, char * previous_qname, char * previous_qname_pairing, char * buffer, SequencesWriter * seqWriteInfo) {$/;"	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,$/;"	f
writeToFormattedWriter	utility.c	/^void writeToFormattedWriter(FormattedWriter * writer, char * format, ...) {$/;"	f
