bloodAGENT/CFastqCreator.cpp at master · ikmb/bloodAGENT · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */

/*
 * File:   CFastqCreator.cpp
 * Author: mwittig
 *
 * Created on August 2, 2019, 12:31 PM
 */
#include <cstdlib>
#include <vector>
#include <map>
#include <set>
#include <string>
#include <libgen.h>

#include <regex>
#include <iterator>

#include "meinetools.h"
#include "CFastqCreator.h"

using namespace std;

CFastqCreator::CFastqCreator(const std::string& filename)
{
    m_fa = CMultiFasta(filename);
}

CFastqCreator::CFastqCreator(const CFastqCreator& orig)
{

}

CFastqCreator::~CFastqCreator() {
}

void CFastqCreator::makePacBioRead(int minSize, int maxSize, int coverage, std::string filename)
{
    ofstream R1(filename.c_str());

    if(!R1 )
    {
        cerr << "could not create output files" << endl;
        exit(EXIT_FAILURE);
    }

    // Write header
    R1 << "@HD\tVN:1.5\tSO:unknown\tpb:3.0.1" << endl;
    R1 << "@RG\tID:a92d5a0b\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=101-500-400;SEQUENCINGKIT=101-427-800;BASECALLERVERSION=5.0.0;FRAMERATEHZ=100.000000;BarcodeFile=/opt/pacbio/smrtlink/userdata/jobs_root/000/000065/pacbio-barcodes/c51caf4d_0a32_4cbd_a508_3e92ccf4589b_index_pacbio_univ/barcodeset.xml;BarcodeHash=fef9cfb8d4d08f346f0dbfec2e5e3ae4;BarcodeCount=2;BarcodeMode=Symmetric;BarcodeQuality=Score\tPU:m54349_190510_125704\tPM:SEQUEL" << endl;
    R1 << "@PG\tID:ccs-3.4.1\tPN:ccs\tVN:3.4.1\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs ccs --minLength=1500 --maxLength=18000 --numThreads=15 --force --minPasses=5 /inPath/bc1001.bam in_silico_generated.bam" << endl;

    if(minSize < maxSize)
        swap(minSize,maxSize);

    int counter = 1;
    for(CMultiFasta::const_iterator i = m_fa.begin(); i != m_fa.end(); i++)
    {
        string name = i->first;
        string seq = i->second;

        int tilings = ((seq.size()/ (minSize+(maxSize-minSize)/2) )+1)*coverage;
        while(tilings-- != 0)
        {
            int fragment_size = minSize + rand() % (( maxSize + 1 ) - minSize);
            int ref_start = rand() % ( seq.length()-fragment_size + 1 );

            string fragment = seq.substr(ref_start,fragment_size);

           R1 << "m54349_190510_125704/1"   << std::setfill('0') << std::setw(6)  << counter << "/ccs\t4\t*\t0\t255\t*\t*\t0\t0\t";
           R1 << seq.substr(ref_start,fragment_size) << '\t' << string(fragment_size,'~') << '\t';
           R1 << "RG:Z:a92d5a0b\tbc:B:S,0,0\tbq:i:85\tnp:i:18\trq:f:0.999881\tsn:B:f,4.86057,9.51716,4.88941,8.44968\tt1:f:1.109\tt2:f:0.041\tt3:f:6.429\tzm:i:1" << std::setfill('0') << std::setw(6)  << counter << endl;
           counter++;
        }


    }
    R1.close();
}

void CFastqCreator::makeIlluminaPairedEnd(int minInsert, int maxInsert, int readLength, int coverage, std::string basename)
{

    ofstream R1(string(basename).append("_R1.fastq").c_str());
    ofstream R2(string(basename).append("_R2.fastq").c_str());


    if(maxInsert < minInsert)
        swap(minInsert,maxInsert);

    if(minInsert < readLength)
    {
        cerr << "Min insert size must be >= readLength. Exit." << endl;
        exit(EXIT_FAILURE);
    }

    if(!R1 || !R2)
    {
        cerr << "could not create output files" << endl;
        exit(EXIT_FAILURE);
    }

    int ref_counter = 1;
    string qualities = string(readLength,'~');
    for(CMultiFasta::const_iterator i = m_fa.begin(); i != m_fa.end(); i++)
    {
        string name = i->first;
        string seq = i->second;

        int tilings = ((seq.size()/readLength)+1)*coverage;
        int inner_counter=0;

        while(tilings-- != 0)
        {
            int insert_size = minInsert + rand() % (( maxInsert + 1 ) - minInsert);
            int ref_start = rand() % ( seq.length()-insert_size + 1 );

            string fragment = seq.substr(ref_start,insert_size);


           R1 << "@HWI-ST778:164:D2C3NACXX:7:1101:"  << std::setfill('0') << std::setw(4) << ref_counter << ':' << std::setfill('0') << std::setw(4) << ++inner_counter << " 1:N:0:TCTTCACA" << endl;
           R1 << fragment.substr(0,readLength) << endl << '+' << endl;
           R1 << qualities << endl;
           R2 << "@HWI-ST778:164:D2C3NACXX:7:1101:"  << std::setfill('0') << std::setw(4) << ref_counter << ':' << std::setfill('0') << std::setw(4) << inner_counter << " 2:N:0:TCTTCACA" << endl;
           R2 << fragment.substr(fragment.length()-readLength) << endl << '+' << endl;
           R2 << qualities << endl;
        }
        ref_counter++;

    }
    R1.close();
    R2.close();
}