BGI/SOAPdenovo2/standardPregraph/inc/extfunc.h

   1 /*
   2  * inc/extfunc.h
   3  *
   4  * Copyright (c) 2008-2012 BGI-Shenzhen <soap at genomics dot org dot cn>.
   5  *
   6  * This file is part of SOAPdenovo.
   7  *
   8  * SOAPdenovo is free software: you can redistribute it and/or modify
   9  * it under the terms of the GNU General Public License as published by
  10  * the Free Software Foundation, either version 3 of the License, or
  11  * (at your option) any later version.
  12  *
  13  * SOAPdenovo is distributed in the hope that it will be useful,
  14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16  * GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
  20  *
  21  */
  22
  23 #include "check.h"
  24 #include "extfunc2.h"
  25
  26 extern void initAIO ( struct aiocb * aio, char * buf, int fd, int size );
  27 extern int AIORead ( struct aiocb * mycb, int * offset, char * buf, char * cach, int * rt, int curr_type );
  28 extern boolean check_file ( char * name ); //add 2012.7.6
  29 extern boolean checkFiles4Scaff ( char * infile );
  30
  31 extern boolean openNextFile ( int * libNo, boolean pairs, unsigned char asm_ctg );
  32 extern int nextValidIndex ( int libNo, boolean pair, unsigned char asm_ctg );
  33 extern void openFileInLib ( int libNo );
  34 extern void closeFp1InLab ( int libNo );
  35 extern void closeFp2InLab ( int libNo );
  36 extern boolean readseqInLib ( char * src_seq, char * src_name, int * len_seq, char * buf, int * start, int offset, int i );
  37
  38 extern void readseq1by1 ( char * src_seq, char * src_name, int * len_seq, FILE * fp, long long num_seq );
  39 extern void readseqPbyP ( char * src_seq, char * src_name, int * insertS, int * len_seq, FILE * fp, long long num_seq );
  40 extern long long readseqpar ( int * max_len, int * min_leg, int * max_name_len, FILE * fp );
  41 extern void free_edge_list ( EDGE_PT * el );
  42 extern void reverseComplementSeq ( char * seq, int len, char * bal_seq );
  43 extern void free_edge_array ( EDGE * ed_array, int ed_num );
  44 extern void free_lightctg_array ( LIGHTCTG * ed_array, int ed_num );
  45 extern char getCharInTightString ( char * tightSeq, int pos );
  46 extern void writeChar2tightSting ( char nt, char * tightSeq, int pos );
  47 extern void short_reads_sum();
  48 extern void read_one_sequence ( FILE * fp, long long * T, char ** X );
  49 extern void output_edges ( preEDGE * ed_array, int ed_num, char * outfile );
  50 extern void loadVertex ( char * graphfile );
  51 extern void loadEdge ( char * graphfile );
  52 extern boolean loadPath ( char * graphfile );
  53 extern READINTERVAL * allocateRV ( int readid, int edgeid );
  54 extern void createRVmemo();
  55 extern void dismissRV ( READINTERVAL * rv );
  56 extern void destroyReadIntervMem();
  57 extern void destroyConnectMem();
  58 extern void u2uConcatenate();
  59 extern void output_contig ( EDGE * ed_array, unsigned int ed_num, char * outfile, int cut_len );
  60 extern void printTightString ( char * tightSeq, int len );
  61 extern int roughUniqueness ( unsigned int edgeno, char ignore_cvg, char * ignored );
  62 extern void outputReadPos ( char * graphfile, int min_len );
  63 extern void testSearch();
  64 extern void allpathConcatenate();
  65 extern void output_updated_edges ( char * outfile );
  66 extern void output_updated_vertex ( char * outfile );
  67 extern void loadUpdatedEdges ( char * graphfile );
  68 extern void loadUpdatedVertex ( char * graphfile );
  69 extern void connectByPE ( char * infile );
  70 extern void output_cntGVZ ( char * outfile );
  71 extern void output_graph ( char * outfile );
  72 extern void testLinearC2C();
  73 extern void output_contig_graph ( char * outfile );
  74 extern void scaffolding ( unsigned int cut_len, char * outfile );
  75 extern int cmp_int ( const void * a, const void * b );
  76 extern CONNECT * allocateCN ( unsigned int contigId, int gap );
  77 extern int recoverRep();
  78 extern void loadPEgrads ( char * infile );
  79 extern int putInsertS ( long long readid, int size, int * currGrads );
  80 extern int getInsertS ( long long readid, int * readlen );
  81 extern int connectByPE_grad ( FILE * fp, int peGrad, char * line );
  82 extern int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line );
  83 extern void PEgradsScaf ( char * infile );
  84 extern void reorderAnnotation ( char * infile, char * outfile );
  85 extern void output_1edge ( preEDGE * edge, gzFile * fp );
  86 extern void prlRead2edge ( char * libfile, char * outfile );
  87 extern void annotFileTrans ( char * infile, char * outfile );
  88 extern void prlLoadPath ( char * graphfile );
  89 extern void misCheck ( char * infile, char * outfile );
  90 extern int uniqueLenSearch ( unsigned int * len_array, unsigned int * flag_array, int num, unsigned int target );
  91 extern int cmp_vertex ( const void * a, const void * b );
  92 extern void linkContig2Vts();
  93 extern int connectByPE_gradPatch ( FILE * fp1, FILE * fp2, int peGrad, char * line1, char * line2 );
  94 extern void scaftiging ( char * graphfile, int len_cut );
  95 extern void gapFilling ( char * graphfile, int cut_len );
  96 extern ARC * getArcBetween ( unsigned int from_ed, unsigned int to_ed );
  97 extern void bubblePinch ( double simiCutoff, char * outfile, int M, boolean isIter, boolean last );
  98 extern void linearConcatenate ( boolean isIter, boolean last );
  99 extern unsigned char setArcMulti ( unsigned int from_ed, unsigned int to_ed, unsigned char value );
 100 extern ARC * allocateArc ( unsigned int edgeid );
 101 extern void cutTipsInGraph ( int cutLen, boolean strict, boolean last );
 102 extern ARC * deleteArc ( ARC * arc_list, ARC * arc );
 103 extern void compactEdgeArray();
 104 extern void dismissArc ( ARC * arc );
 105 extern void createArcMemo();
 106 extern ARC * getArcBetween ( unsigned int from_ed, unsigned int to_ed );
 107 extern ARC * allocateArc ( unsigned int edgeid );
 108 extern void writeChar2tightString ( char nt, char * tightSeq, int pos );
 109 extern void output_heavyArcs ( char * outfile );
 110 extern preARC * allocatePreArc ( unsigned int edgeid );
 111 extern void destroyPreArcMem();
 112 extern void traceAlongArc ( unsigned int destE, unsigned int currE, int max_steps, int min, int max, int index, int len, int * num_route );
 113 extern void freeContig_array();
 114 extern void output_scafSeq ( char * graphfile, int len_cut );
 115 extern void putArcInHash ( unsigned int from_ed, unsigned int to_ed );
 116 extern boolean DoesArcExist ( unsigned int from_ed, unsigned int to_ed );
 117 extern void recordArcInHash();
 118 extern void destroyArcHash();
 119 extern void removeWeakEdges ( int lenCutoff, unsigned int multiCutoff );
 120 extern void createArcLookupTable();
 121 extern void deleteArcLookupTable();
 122 extern void putArc2LookupTable ( unsigned int from_ed, ARC * arc );
 123 extern void removeArcInLookupTable ( unsigned int from_ed, unsigned int to_ed );
 124 extern ARC * arcCount ( unsigned int edgeid, unsigned int * num );
 125 extern void mapFileTrans ( char * infile );
 126 extern void solveReps();
 127 extern void removeDeadArcs();
 128 extern void destroyArcMem();
 129 extern void getCntsInFile ( char * infile );
 130 extern void scafByCntInfo ( char * infile );
 131 extern CONNECT * add1Connect ( unsigned int e1, unsigned int e2, int gap, int weight, boolean inherit );
 132 extern void getScaff ( char * infile );
 133 extern void traceAlongMaskedCnt ( unsigned int destE, unsigned int currE, int max_steps, int min, int max, int index, int len, int * num_route );
 134 extern void createPreArcMemManager();
 135 extern boolean loadPathBin ( char * graphfile );
 136 extern void recordArcsInLookupTable();
 137 extern FILE * multiFileRead1seq ( char * src_seq, char * src_name, int * len_seq, FILE * fp, FILE * freads );
 138 extern void multiFileSeqpar ( FILE * fp );
 139 extern long long multiFileParse ( int * max_leg, int * min_leg, int * max_name_leg, FILE * fp );
 140 extern CONNECT * getCntBetween ( unsigned int from_ed, unsigned int to_ed );
 141 extern void createCntMemManager();
 142 extern void destroyConnectMem();
 143 extern void createCntLookupTable();
 144 extern void deleteCntLookupTable();
 145 extern void putCnt2LookupTable ( unsigned int from_c, CONNECT * cnt );
 146 extern void prlRead2Ctg ( char * seqfile, char * outfile );
 147 extern boolean prlContig2nodes ( char * grapfile, int len_cut );
 148 extern void scan_libInfo ( char * libfile );
 149 extern void free_libs();
 150
 151 extern boolean read1seqInLibBam ( char * src_seq, char * src_name, int * len_seq, int * libNo, boolean pair, unsigned char asm_ctg, int * type );
 152 extern boolean read1seqInLib ( char * src_seq, char * src_name, int * len_seq,
 153                                int * libNo, boolean pair, unsigned char asm_ctg , int * type );
 154 extern void save4laterSolve();
 155 extern void solveRepsAfter();
 156 extern void free_pe_mem();
 157 extern void alloc_pe_mem ( int gradsCounter );
 158 extern void prlDestroyPreArcMem();
 159 extern preARC * prlAllocatePreArc ( unsigned int edgeid, MEM_MANAGER * manager );
 160 extern boolean prlRead2HashTable ( char * libfile, char * outfile );
 161 extern void free_allSets();
 162 extern void removeSingleTips();
 163 extern void removeMinorTips();
 164 extern void kmer2edges ( char * outfile );
 165 extern void output_vertex ( char * outfile );
 166 extern boolean prlRead2HashTable ( char * libfile, char * outfile );
 167 extern void Links2Scaf ( char * infile );
 168 extern void PE2Links ( char * infile );
 169 extern unsigned int getTwinCtg ( unsigned int ctg );
 170 extern void basicContigInfo ( char * infile );
 171 extern boolean isSmallerThanTwin ( unsigned int ctg );
 172 extern boolean isLargerThanTwin ( unsigned int ctg );
 173 extern boolean isSameAsTwin ( unsigned int ctg );
 174 extern boolean loadMarkerBin ( char * graphfile );
 175 extern void readsCloseGap ( char * graphfile );
 176 extern void prlReadsCloseGap ( char * graphfile );
 177 extern void locateReadOnScaf ( char * graphfile );
 178 /*********** Kmer related *************/
 179 extern Kmer createFilter ( int overlaplen );
 180 extern void printKmerSeq ( FILE * fp, Kmer kmer );
 181 //extern U256b Kmer2int256(Kmer seq);
 182 extern boolean KmerLarger ( Kmer kmer1, Kmer kmer2 );
 183 extern boolean KmerSmaller ( Kmer kmer1, Kmer kmer2 );
 184 extern boolean KmerEqual ( Kmer kmer1, Kmer kmer2 );
 185 extern Kmer KmerAnd ( Kmer kmer1, Kmer kmer2 );
 186 extern Kmer KmerLeftBitMoveBy2 ( Kmer word );
 187 extern Kmer KmerRightBitMoveBy2 ( Kmer word );
 188 extern Kmer KmerPlus ( Kmer prev, char ch );
 189 extern Kmer nextKmer ( Kmer prev, char ch );
 190 extern Kmer prevKmer ( Kmer next, char ch );
 191 extern char firstCharInKmer ( Kmer kmer );
 192 extern Kmer KmerRightBitMove ( Kmer word, int dis );
 193 extern Kmer reverseComplement ( Kmer word, int overlap );
 194 extern ubyte8 hash_kmer ( Kmer kmer );
 195 extern int kmer2vt ( Kmer kmer );
 196 extern void print_kmer ( FILE * fp, Kmer kmer, char c );
 197 extern int bisearch ( VERTEX * vts, int num, Kmer target );
 198 extern void printKmerSeq ( FILE * fp, Kmer kmer );
 199 extern char lastCharInKmer ( Kmer kmer );
 200 int localGraph ( READNEARBY * rdArray, int num, CTGinSCAF * ctg1, CTGinSCAF * ctg2,
 201                  int origOverlap, Kmer * kmerCtg1, Kmer * kmerCtg2,
 202                  int overlap, DARRAY * gapSeqArray, char * seqCtg1, char * seqCtg2, char * seqGap );
 203 extern unsigned int getTwinEdge ( unsigned int edgeno );
 204 extern boolean EdSmallerThanTwin ( unsigned int edgeno );
 205 extern boolean EdLargerThanTwin ( unsigned int edgeno );
 206 extern boolean EdSameAsTwin ( unsigned int edgeno );
 207 extern void removeLowCovEdges ( int lenCutoff, unsigned short covCutoff, boolean last );
 208 extern int getMaxLongReadLen ( int num_libs );
 209 extern void prlLongRead2Ctg ( char * libfile, char * outfile );
 210 extern void outputTightStr ( FILE * fp, char * tightStr, int start, int length, int outputlen, int revS, int * col );
 211 extern void crc32c_Init();
 212
 213 extern int validArcCount ( preARC * arc, int cutoff );
 214 extern unsigned int maxArcWeight ( preARC * arc );
 215 extern __uint128_t Kmer2int128 ( Kmer seq );
 216 extern void printSeq ( FILE * fo, char * seq, int len );
 217