c_cpp/etc/mVicuna/src/SeqFrqEst.h

   1 //========================================================================
   2 // Project     : M-Vicuna
   3 // Name        : SeqFrqEst.h
   4 // Author      : Xiao Yang
   5 // Created on  : Aug 6, 2013
   6 // Version     : 1.0
   7 // Copyright   : The Broad Institute
   8 //                               SOFTWARE COPYRIGHT NOTICE AGREEMENT
   9 //                               This software and its documentation are copyright (2013)
  10 //                               by the Broad Institute. All rights are reserved.
  11 //
  12 //                               This software is supplied without any warranty or
  13 //                               guaranteed support whatsoever. The Broad Institute cannot
  14 //                               be responsible for its use,    misuse, or functionality.
  15 // Description :
  16 //========================================================================
  17
  18
  19 #ifndef SEQFRQEST_H_
  20 #define SEQFRQEST_H_
  21
  22 #include "xutil.h"
  23 #include "ReadBioFile.h"
  24 #include "jaz/fastx_iterator.hpp"
  25 #include "xny/seq_manip.hpp"
  26 #include "xny/file_manip.hpp"
  27
  28 void estSeqFrq (const strvec_t& ipfqlist, const strvec_t& isfqlist,
  29                 int k, int batch, bool silent);
  30
  31 void obtain_kfrq (umap_t& kcnt, int k, int batch, const strvec_t& files, bool silent);
  32 void kmer_cnt_in_seqs (umap_t& kcnt,    const strvec_t& seqs, int k);
  33
  34
  35 void obtain_seqfrq (ivec_t& frq, const umap_t& kcnt,    int k,
  36                 int batch, const strvec_t& files, bool silent) ;
  37 void seq_freq (ivec_t& frq, const umap_t& kcnt, int k, const strvec_t& seqs);
  38
  39 #endif /* SEQFRQEST_H_ */