BGI/SOAPsnp/tools.h

   1 /*
   2  ******************************************************************************
   3  *Copyright 2010
   4  *      BGI-SHENZHEN
   5  *All Rights Reserved
   6  *ATHUOR : Bill Tang
   7  *CREATE DATE : 2010-7-14
   8  *CLASS NAME:
   9  *FUNCTION : some useful function to the SOAPsnp
  10  *FILE NAME : tool.h
  11  *UPDATE DATE : 2010-8-3
  12  *UPDATE BY : Bill Tang
  13  *UPDATE DATE : 2010-9-6
  14  *UPDATE BY :Zhou Guyue
  15  *UPDATE: 2010-10-15 change the struct SFS_PARA, add a member qs.
  16  *******************************************************************************
  17  */
  18 #ifndef TOOLS_H
  19 #define TOOLS_H
  20
  21 #include <iostream>
  22 #include <strstream>
  23 #include <vector>
  24 #include <string>
  25 #include <sstream>
  26 #include <fstream>
  27 #include <cassert>
  28 using namespace std;
  29 typedef ifstream my_ifstream;
  30
  31 #define NOUSE_ALIGNMENT "alignment is no use"
  32 #define HIT_COUNT_X0            "X0:i:"
  33 #define HIT_COUNT_H0            "H0:i:"
  34 #define SFS_PARA_ERROR   -1              //if sfs para is wrong return SFS_PARA_ERROR
  35 #define SFS_PARA_SUCC    1                               //if sfs para is right return SFS_PARA_SUCC
  36
  37
  38 /* integer to string*/
  39 std::string myitoa(int num);
  40 // A function to spilt string s into vector vec according to char splitchar
  41 void StringSplit(std::string s, char splitchar, std::vector<std::string>& vec);
  42 /* count the indel length from the cigar string. return the indel length and the position*/
  43 int count_indel_len(const std::string cigar, int &pos);
  44 /* format the sam text to the soap text*/
  45 std::string alignment_format(const std::string &sam_ali);
  46
  47 /*a struct for sfs parament*/
  48 typedef struct
  49 {
  50         int doBay;                      // 0:not Bay£¬1:do Bay£¬default is 0
  51         int doJoint;                    //0:not Joint£¬1:do Joint£¬default is 0
  52         int writeFr;            // 0:not write Fr, 1: write Fr, default is 0
  53         std::string outfiles;           //out files path
  54         int start_pos;  // start position
  55         int stop_pos;   // stop position
  56         int under_FP;           // 0: not under Flow Protect £¬1:under Flow Protect£¬default is 0
  57         int allow_PathZ;                // 0: notallow Phat Zero£¬1:allow Phat ZeroÊÇ£¬default is 0
  58         double bias;    // default bias is 0.03
  59         double pvar;    // The probability for beeing variable in the population£¬default is 0.015
  60         double eps;     //error rate  ,default is 0.005
  61         double pThres ;         //select the out put threshold of snp £¬default is 0.01
  62         int sigle_MJ;    // 0:not sigle minor joint£¬1:sigle minor joint£¬default is 0
  63         int sigle_MB;    //0: not sigle minor bay£¬1: sigle minor bay£¬default is  0
  64         int alternative; //
  65         int jointFold;  //
  66         int qs; // the quality score threshold.
  67         std::string faiPath; // fai file's path.
  68         //update 11-29
  69         int sfs_first_last; // 0: output h[0]~h[2k] , 1:output h[0] and h[2k]
  70 }SFS_PARA ;
  71
  72 /*initialize a sfs_para struct*/
  73 #define sfs_init()(new SFS_PARA)
  74 /*destroy a sfs_para struct*/
  75 #define sfs_destroy(b) do {if (b) { delete b; }} while (0)
  76 /*sfs help information*/
  77 void sfs_info(void);
  78 /* initialize sfs parament*/
  79 int init_sfs_para(const string sfs_path, SFS_PARA *sfs );
  80 /*change string to bool*/
  81 int str_bool( const char* str);
  82 /* count soft clip number at the beginning*/
  83 int count_soft_clip(const std::string cigar, int &last_S);
  84
  85 #endif