10 int uchime_main(int, char**);
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17 vector<char> m_RecTypes;
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18 vector<float> m_PctIds;
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19 vector<const char *> m_Labels;
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20 vector<const char *> m_SeedLabels;
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21 vector<unsigned> m_SeedIndexes;
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22 vector<const char *> m_CompressedPaths;
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23 vector<unsigned> m_SeqLengths;
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24 vector<unsigned> m_SortOrder;
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25 vector<char> m_Strands;
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26 vector<unsigned> m_Los;
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27 vector<unsigned> m_SeedLos;
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30 /* some function prototypes */
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34 void Clear(bool ctor = false);
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36 void FromFile(const string &FileName);
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37 void FromClstr(const string &FileName);
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38 void ToFile(const string &FileName);
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39 unsigned GetRecordCount() const;
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41 void ToClstr(const string &FileName);
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42 void ToFasta(const string &FileName, const SeqDB &Input, bool Reformat);
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43 void Create(const string &FileName);
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47 void WriteNotMatched(unsigned L, const char *Label) const;
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48 void WriteLibSeed(unsigned SeedIndex, unsigned L, const char *Label) const;
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49 void WriteNewSeed(unsigned SeedIndex, unsigned L, const char *Label) const;
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50 void WriteHit(const SeqData &SA, const SeqData &SB, double FractId,
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51 const PathData &PD) const;
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52 void WriteReject(const SeqData &SA, const SeqData &SB, double FractId,
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53 const char *Path) const;
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54 void WriteHit(unsigned SeedIndex, unsigned L, double PctId,
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55 const char *CompressedPath, char Strand, unsigned Lo, unsigned SeedLo,
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56 const char *Label, const char *SeedLabel) const;
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57 void WriteHit(const AlnData &AD);
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58 void WriteLibCluster(unsigned SeedIndex, unsigned Size, double AvgId,
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59 const char *Label) const;
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60 void WriteNewCluster(unsigned SeedIndex, unsigned Size, double AvgId,
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61 const char *Label) const;
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62 void WriteSeqX(FILE *f, const byte *Seq, unsigned L, const char *CompressedPath) const;
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