c_cpp/etc/mVicuna/src/ReadBioFile.h

   1 //========================================================================
   2 // Project     : M-Vicuna
   3 // Name        : ReadBioFile.h
   4 // Author      : Xiao Yang
   5 // Created on  : Jun 4, 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 READBIOFILE_H_
  20 #define READBIOFILE_H_
  21
  22 #include "xutil.h"
  23 #include "jaz/fastx_iterator.hpp"
  24
  25 void add_fq_reads (std::vector<fqtuple_t>& seq, int num,
  26         bio::fastq_input_iterator<>& iter, bio::fastq_input_iterator<> end);
  27
  28 void add_fq_reads_only (strvec_t& seq, int num,
  29         bio::fastq_input_iterator<>& iter, bio::fastq_input_iterator<> end);
  30
  31 void add_fa_reads (std::vector<strpair_t>& seq, int num,
  32         bio::fasta_input_iterator<>& iter, bio::fasta_input_iterator<> end);
  33
  34 void add_fa_reads_only (strvec_t& seq, int num,
  35         bio::fasta_input_iterator<>& iter, bio::fasta_input_iterator<> end);
  36 #endif /* READBIOFILE_H_ */