/***************************************************************************
 * Title:          extfunc.h
 * Author:         Haixu Tang
 * Created:        Jun. 2002
 * Last modified:  May. 2004
 *
 * Copyright (c) 2001-2004 The Regents of the University of California
 * All Rights Reserved
 * See file LICENSE for details.
 ***************************************************************************/
#include "check.h"
#include "extfunc2.h"
extern NODE **seq2nodes_with_pair(char *seqfile, char *outfile);
extern NODE **prlSeq2nodes_with_pair(char *seqfile, char *outfile);
extern void readseq1by1(char *src_seq, char *src_name, int *len_seq, FILE *fp, long long num_seq);
extern void readseqPbyP(char *src_seq, char *src_name, int *insertS, int *len_seq, FILE *fp, long long num_seq);
extern void nodes2edges_with_pair(NODE **hash_table, EDGE_PT **edge_list, char *outfile);
extern int findOrInsertOccurenceInNodeTree(Kmer kmer, NODE **T);
extern NODE *SplayNodeTree(NODE *T, Kmer kmer);
extern Kmer reverseComplement(Kmer word, int overlap);
extern Kmer hash_kmer(Kmer kmer);
extern void link2next(NODE *node, char ch);
extern unsigned char check_link2next(NODE *node, char ch);
extern void unlink2next(NODE *node, char ch);
extern void link2prev(NODE *node, char ch);
extern unsigned char check_link2prev(NODE *node, char ch);
extern void unlink2prev(NODE *node, char ch);
extern int count_link2next(NODE *node);
extern int count_link2prev(NODE *node);
extern Kmer nextKmer(Kmer prev, char ch);
extern Kmer prevKmer(Kmer next, char ch);
extern long long readseqpar(int *max_len, int *min_leg, int *max_name_len, FILE *fp);
extern void destroyNodeHash(NODE **hash_table);
extern void free_edge_list(EDGE_PT *el);
extern void reverseComplementSeq(char *seq, int len, char *bal_seq);
extern void free_node_list(NODE_PT *np);
extern NODE *SplayNodeTree_FILTER(NODE *T, Kmer kmer);
extern NODE *allocateNode_cvg(Kmer kmer);
extern int findOrInsertOccurenceInNodeTree_cvg(Kmer kmer, NODE **T);
extern void free_edge_array(EDGE *ed_array, int ed_num);
extern void free_lightctg_array(LIGHTCTG *ed_array, int ed_num);
extern char getCharInTightString(char *tightSeq, int pos);
extern void writeChar2tightSting(char nt, char *tightSeq, int pos);
extern void short_reads_sum();
extern void read_one_sequence(FILE *fp, long long *T, char **X);
extern void output_edges(preEDGE *ed_array, int ed_num, char *outfile);
extern void read2edge(char *seqfile, NODE **hash_table, char *outfile);
extern void loadVertex(char *graphfile);
extern int kmer2vt(Kmer kmer);
extern void loadEdge(char *graphfile);
extern boolean loadPath(char *graphfile);
extern READINTERVAL *allocateRV(int readid, int edgeid);
extern void createRVmemo();
extern void dismissRV(READINTERVAL *rv);
extern void destroyReadIntervMem();
extern void destroyConnectMem();
extern void u2uConcatenate();
extern void unlink2all(NODE *node, NODE **hash_table);
extern void cutTip(NODE **hash_table);
extern void output_contig(EDGE *ed_array, unsigned int ed_num, char *outfile, int cut_len);
extern void printTightString(char *tightSeq, int len);
extern int roughUniqueness(unsigned int edgeno, char ignore_cvg, char *ignored);
extern void outputReadPos(char *graphfile, int min_len);
extern NODE *reverseComplementNode(NODE *node1, NODE **hash_table);
extern void testSearch();
extern void print_kmer(FILE *fp, Kmer kmer, char c);
extern void allpathConcatenate();
extern void output_updated_edges(char *outfile);
extern void output_updated_vertex(char *outfile);
extern void loadUpdatedEdges(char *graphfile);
extern void loadUpdatedVertex(char *graphfile);
extern void connectByPE(char *infile);
extern void output_cntGVZ(char *outfile);
extern void output_graph(char *outfile);
extern void removeUnreliable(NODE **hash_talbe);
extern void testLinearC2C();
extern void output_contig_graph(char *outfile);
extern void scaffolding(unsigned int cut_len, char *outfile);
extern int cmp_int(const void *a, const void *b);
extern CONNECT *allocateCN(unsigned int contigId, int gap);
extern int recoverRep();
extern void loadPEgrads(char *infile);
extern int putInsertS(long long readid, int size, int *currGrads);
extern int getInsertS(long long readid, int *readlen);
extern int connectByPE_grad(FILE *fp, int peGrad, char *line);
extern void PEgradsScaf(char *infile);
extern void reorderAnnotation(char *infile, char *outfile);
extern int count_ends(NODE **hash_table);
extern void output_1edge(preEDGE *edge, FILE *fp);
extern void prlRead2edge(char *libfile, char *outfile);
extern int count_edges(NODE **hash_table);
extern int prlFindOrInsertOccurenceInNodeTree_cvg(Kmer kmer, NODE **T, MEM_MANAGER *node_mem_manager);
extern void prlDestroyNodeHash(NODE **hash_table);
extern void annotFileTrans(char *infile, char *outfile);
extern void prlLoadPath(char *graphfile);
extern void misCheck(char *infile, char *outfile);
extern int uniqueLenSearch(unsigned int *len_array, unsigned int *flag_array, int num, unsigned int target);
extern int cmp_vertex(const void *a, const void *b);
extern void linkContig2Vts();
extern int bisearch(VERTEX *vts, int num, Kmer target);
extern int connectByPE_gradPatch(FILE *fp1, FILE *fp2, int peGrad, char *line1, char *line2);
extern void scaftiging(char *graphfile, int len_cut);
extern void gapFilling(char *graphfile, int cut_len);
extern ARC *getArcBetween(unsigned int from_ed, unsigned int to_ed);
extern void bubblePinch(double simiCutoff, char *outfile, int M);
extern void linearConcatenate();
extern unsigned char setArcMulti(unsigned int from_ed, unsigned int to_ed, unsigned char value);
extern ARC *allocateArc(unsigned int edgeid);
extern void cutTipsInGraph(int cutLen, boolean strict);
extern ARC *deleteArc(ARC *arc_list, ARC *arc);
extern void compactEdgeArray();
extern void dismissArc(ARC *arc);
extern void createArcMemo();
extern ARC *getArcBetween(unsigned int from_ed, unsigned int to_ed);
extern ARC *allocateArc(unsigned int edgeid);
extern void unlink2prevUncertain(NODE *node, char ch, boolean smaller);
extern char firstCharInKmer(Kmer kmer);
extern void writeChar2tightString(char nt, char *tightSeq, int pos);
extern Kmer reverseComplementVerbose(Kmer word, int overlap);
extern Kmer KmerPlus(Kmer prev, char ch);
extern void output_heavyArcs(char *outfile);
extern preARC *allocatePreArc(unsigned int edgeid);
extern void destroyPreArcMem();
extern void traceAlongArc(unsigned int destE, unsigned int currE, int max_steps, int min, int max, int index, int len, int *num_route);
extern void freeContig_array();
extern void output_scafSeq(char *graphfile, int len_cut);
extern void putArcInHash(unsigned int from_ed, unsigned int to_ed);
extern boolean DoesArcExist(unsigned int from_ed, unsigned int to_ed);
extern void recordArcInHash();
extern void destroyArcHash();
extern void removeWeakEdges(int lenCutoff, unsigned int multiCutoff);
extern void createArcLookupTable();
extern void deleteArcLookupTable();
extern void putArc2LookupTable(unsigned int from_ed, ARC *arc);
extern void removeArcInLookupTable(unsigned int from_ed, unsigned int to_ed);
extern ARC *arcCount(unsigned int edgeid, unsigned int *num);
extern void mapFileTrans(char *infile);
extern void solveReps();
extern void removeDeadArcs();
extern void destroyArcMem();
extern int count_link2prevB(NODE *node);
extern int count_link2nextB(NODE *node);
extern void getCntsInFile(char *infile);
extern void scafByCntInfo(char *infile);
extern CONNECT *add1Connect(unsigned int e1, unsigned int e2, int gap, int weight, boolean inherit);
extern void getScaff(char *infile);
extern void traceAlongMaskedCnt(unsigned int destE, unsigned int currE, int max_steps, int min, int max, int index, int len, int *num_route);
extern void createPreArcMemManager();
extern boolean loadPathBin(char *graphfile);
extern void analyzeTips(NODE **hash_table, char *graphfile);
extern void recordArcsInLookupTable();
extern FILE *multiFileRead1seq(char *src_seq, char *src_name, int *len_seq, FILE *fp, FILE *freads);
extern void multiFileSeqpar(FILE *fp);
extern long long multiFileParse(int *max_leg, int *min_leg, int *max_name_leg, FILE *fp);
extern CONNECT *getCntBetween(unsigned int from_ed, unsigned int to_ed);
extern void createCntMemManager();
extern void destroyConnectMem();
extern void createCntLookupTable();
extern void deleteCntLookupTable();
extern void putCnt2LookupTable(unsigned int from_c, CONNECT *cnt);
extern int prlFindOrInsertOccurenceInEdonTree(Kmer kmer, EDON **T, MEM_MANAGER *node_mem_manager);
extern EDON *SplayEdonTree(EDON *T, Kmer kmer);
extern void prlDestroyEdonHash(EDON **hash_table);
extern void prlRead2Ctg(char *seqfile, char *outfile);
extern void prlLongRead2Ctg(char *libfile, char *outfile);
extern boolean prlContig2nodes(char *grapfile, int len_cut);
extern void scan_libInfo(char *libfile);
extern int getMaxLongReadLen(int num_libs);
extern void free_libs();
extern boolean read1seqInLib(char *src_seq, char *src_name, int *len_seq,
                             int *libNo, boolean pair, unsigned char purpose);
extern NODE **prlEdge2nodes(char *grapfile);
extern void prlRead2graph(char *libfile, NODE **hash_table, char *outfile);
extern void save4laterSolve();
extern void solveRepsAfter();
extern void free_pe_mem();
extern void alloc_pe_mem(int gradsCounter);
extern NODE *searchNodeTree(NODE *T, Kmer kmer);
extern EDON *searchEdonTree(EDON *T, Kmer kmer);
extern void prlDestroyPreArcMem();
extern preARC *prlAllocatePreArc(unsigned int edgeid, MEM_MANAGER *manager);
extern boolean prlRead2HashTable(char *libfile, char *outfile);
extern void free_allSets();
extern void removeSingleTips();
extern void removeMinorTips();
extern void kmer2edges(char *outfile);
extern void output_vertex(char *outfile);
extern boolean prlRead2HashTable(char *libfile, char *outfile);
extern void Links2Scaf(char *infile);
extern void PE2Links(char *infile);
extern void basicContigInfo(char *infile);
extern unsigned int getTwinCtg(unsigned int ctg);
extern boolean isSmallerThanTwin(unsigned int ctg);
extern boolean isLargerThanTwin(unsigned int ctg);
extern boolean isSameAsTwin(unsigned int ctg);
extern boolean loadMarkerBin(char *graphfile);
extern void readsCloseGap(char *graphfile);
extern void prlReadsCloseGap(char *graphfile);
extern void locateReadOnScaf(char *graphfile);
extern unsigned int getTwinEdge(unsigned int edge);
extern boolean EdSmallerThanTwin(unsigned int edge);
extern boolean EdLargerThanTwin(unsigned int edge);
extern boolean EdSameAsTwin(unsigned int edge);
extern void removeLowCovEdges(int lenCutoff, unsigned short covCutoff);
extern int localGraph(READNEARBY *rdArray, int num, CTGinSCAF *ctg1, CTGinSCAF *ctg2,
                      int origOverlap, Kmer *kmerCtg1, Kmer *kmerCtg2,
                      int overlap, DARRAY *gapSeqArray, char *seqCtg1, char *seqCtg2, char *seqGap);