Commit 04b629e9 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tools/segmentD.cpp: remove unused file

This was dead code.
parent 2c14d274
#include <fstream>
#include <iostream>
#include <string>
#include "core/kmerstore.h"
#include "core/dynprog.h"
#include "core/fasta.h"
#include "core/segment.h"
#include <core/affectanalyser.h>
// #include "core/output.h"
using namespace std;
int main(int argc, char* argv[])
{
const char* frep_V = "../../../../seq/Repertoire/IGHV.fa" ;
const char* frep_D = "../../../../seq/Repertoire/IGHD.fa" ;
const char* frep_J = "../../../../seq/Repertoire/IGHJ.fa" ;
const char* fdata_default = "../../../../seq/Stanford_S22_s.fasta" ;
const char* fdata = argc>1 ? argv[1] : fdata_default ;
Fasta data(fdata, 1, " ");
Fasta rep_V(frep_V, 2, "|");
Fasta rep_D(frep_D, 2, "|");
Fasta rep_J(frep_J, 2, "|");
int w = 40 ;
int ch=0;
int tot=0;
//for(int i = 0 ; i < data.size() ; i++)
for(int i = 0 ; i < 10 ; i++)
{
cout << endl ;
cout << endl ;
cout << "=== " << data.label_full(i) << endl ;
cout << endl << "--- FineSegmenter" << endl ;
//segmentation VJ
FineSegmenter s(data.read(i), rep_V, rep_J, 0, 40);
s.FineSegmentD(rep_V, rep_D, rep_J);
//cout << s.info << endl << endl ;
if (s.isSegmented()){
cout << s.info << endl << endl ;
cout << " V :" << s.seg_V << endl ;
cout << " XX D XX :" << s.seg_N1 << " " << s.seg_D << " " << s.seg_N2 <<endl ;
cout << " J :" << s.seg_J << endl ;
cout << "Junction :" << s.getJunction(w) << endl ;
if (s.seg_N1[0]=='o'||s.seg_N2[0]=='o') ch++;
tot++;
}
else{
cout << "fail" << s.info ;
}
}
}
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