/*
 * inc/extfunc.h
 *
 * Copyright (c) 2008-2016 Ruibang Luo <aquaskyline.com>.
 *
 * This file is part of SOAPdenovo.
 *
 * SOAPdenovo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#include "check.h"
#include "extfunc2.h"

extern void initAIO ( struct aiocb *aio, char *buf, int fd, int size );
extern int AIORead ( struct aiocb *mycb, int *offset, char *buf, char *cach, int *rt, int curr_type );
extern boolean check_file ( char *name );  //add 2012.7.6
extern boolean checkFiles4Scaff ( char *infile );

extern boolean openNextFile ( int *libNo, boolean pairs, unsigned char asm_ctg );
extern int nextValidIndex ( int libNo, boolean pair, unsigned char asm_ctg );
extern void openFileInLib ( int libNo );
extern void closeFp1InLab ( int libNo );
extern void closeFp2InLab ( int libNo );
extern boolean readseqInLib ( char *src_seq, char *src_name, int *len_seq, char *buf, int *start, int offset, int i );

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 long long readseqpar ( int *max_len, int *min_leg, int *max_name_len, FILE *fp );
extern void free_edge_list ( EDGE_PT *el );
extern void reverseComplementSeq ( char *seq, int len, char *bal_seq );
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 loadVertex ( char *graphfile );
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 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 void testSearch();
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 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 int connectByPE_grad_gz ( gzFile *fp, int peGrad, char *line );
extern void PEgradsScaf ( char *infile );
extern void reorderAnnotation ( char *infile, char *outfile );
extern void output_1edge ( preEDGE *edge, gzFile *fp );
extern void prlRead2edge ( char *libfile, char *outfile );
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 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, boolean isIter, boolean last );
extern void linearConcatenate ( boolean isIter, boolean last );
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, boolean last );
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 writeChar2tightString ( char nt, char *tightSeq, int pos );
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 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 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 void prlRead2Ctg ( char *seqfile, char *outfile );
extern boolean prlContig2nodes ( char *grapfile, int len_cut );
extern void scan_libInfo ( char *libfile );
extern void free_libs();

extern boolean read1seqInLibBam ( char *src_seq, char *src_name, int *len_seq, int *libNo, boolean pair, unsigned char asm_ctg, int *type );
extern boolean read1seqInLib ( char *src_seq, char *src_name, int *len_seq,
                               int *libNo, boolean pair, unsigned char asm_ctg , int *type );
extern void save4laterSolve();
extern void solveRepsAfter();
extern void free_pe_mem();
extern void alloc_pe_mem ( int gradsCounter );
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 unsigned int getTwinCtg ( unsigned int ctg );
extern void basicContigInfo ( char *infile );
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 );
/*********** Kmer related *************/
extern Kmer createFilter ( int overlaplen );
extern void printKmerSeq ( FILE *fp, Kmer kmer );
//extern U256b Kmer2int256(Kmer seq);
extern boolean KmerLarger ( Kmer kmer1, Kmer kmer2 );
extern boolean KmerSmaller ( Kmer kmer1, Kmer kmer2 );
extern boolean KmerEqual ( Kmer kmer1, Kmer kmer2 );
extern Kmer KmerAnd ( Kmer kmer1, Kmer kmer2 );
extern Kmer KmerLeftBitMoveBy2 ( Kmer word );
extern Kmer KmerRightBitMoveBy2 ( Kmer word );
extern Kmer KmerPlus ( Kmer prev, char ch );
extern Kmer nextKmer ( Kmer prev, char ch );
extern Kmer prevKmer ( Kmer next, char ch );
extern char firstCharInKmer ( Kmer kmer );
extern Kmer KmerRightBitMove ( Kmer word, int dis );
extern Kmer reverseComplement ( Kmer word, int overlap );
extern ubyte8 hash_kmer ( Kmer kmer );
extern int kmer2vt ( Kmer kmer );
extern void print_kmer ( FILE *fp, Kmer kmer, char c );
extern int bisearch ( VERTEX *vts, int num, Kmer target );
extern void printKmerSeq ( FILE *fp, Kmer kmer );
extern char lastCharInKmer ( Kmer kmer );
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 );
extern unsigned int getTwinEdge ( unsigned int edgeno );
extern boolean EdSmallerThanTwin ( unsigned int edgeno );
extern boolean EdLargerThanTwin ( unsigned int edgeno );
extern boolean EdSameAsTwin ( unsigned int edgeno );
extern void removeLowCovEdges ( int lenCutoff, unsigned short covCutoff, boolean last );
extern int getMaxLongReadLen ( int num_libs );
extern void prlLongRead2Ctg ( char *libfile, char *outfile );
extern void outputTightStr ( FILE *fp, char *tightStr, int start, int length, int outputlen, int revS, int *col );
extern void crc32c_Init();

extern int validArcCount ( preARC *arc, int cutoff );
extern unsigned int maxArcWeight ( preARC *arc );
extern __uint128_t Kmer2int128 ( Kmer seq );
extern void printSeq ( FILE *fo, char *seq, int len );