c_cpp/etc/mVicuna/src/ReadBioFile.cpp

   1 //========================================================================
   2 // Project     : M-Vicuna
   3 // Name        : ReadBioFile.cpp
   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 #include "ReadBioFile.h"
  19
  20 /**     Retrieve num records (header, read, qual) from fastq file pointed by
  21  * iter
  22  */
  23 void add_fq_reads (std::vector<fqtuple_t>& seq, int num,
  24         bio::fastq_input_iterator<>& iter, bio::fastq_input_iterator<> end){
  25         int cnt = 0;
  26         for (; iter != end; ++ iter) {
  27                 seq.push_back (*iter);
  28                 ++ cnt;
  29                 if (cnt >= num) {
  30                         ++ iter;
  31                         return;
  32                 }
  33         }
  34 } // add_fq_reads
  35
  36 void add_fq_reads_only (strvec_t& seq, int num,
  37         bio::fastq_input_iterator<>& iter, bio::fastq_input_iterator<> end){
  38         int cnt = 0;
  39         for (; iter != end; ++ iter) {
  40                 seq.push_back (std::get<1>(*iter));
  41                 ++ cnt;
  42                 if (cnt >= num) {
  43                         ++ iter;
  44                         return;
  45                 }
  46         }
  47 }
  48
  49 void add_fa_reads (std::vector<strpair_t>& seq, int num,
  50         bio::fasta_input_iterator<>& iter, bio::fasta_input_iterator<> end){
  51         int cnt = 0;
  52         for (; iter != end; ++ iter) {
  53                 seq.push_back (*iter);
  54                 ++ cnt;
  55                 if (cnt >= num) {
  56                         ++ iter;
  57                         return;
  58                 }
  59         }
  60 } //add_fa_reads
  61
  62 void add_fa_reads_only (strvec_t& seq, int num,
  63         bio::fasta_input_iterator<>& iter, bio::fasta_input_iterator<> end){
  64         int cnt = 0;
  65         for (; iter != end; ++ iter) {
  66                 seq.push_back (iter->second);
  67                 ++ cnt;
  68                 if (cnt >= num) {
  69                         ++ iter;
  70                         return;
  71                 }
  72         }
  73 } //add_fa_reads
  74
  75