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toy implementation of map-based multiple file write #4

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toy implementation of map-based multiple file write #4

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137b679
toy implementation of map-based multiple file write
Dec 9, 2021
fe875e4
removed vscode file
Dec 9, 2021
6c24bc4
added explanatory comment
Dec 9, 2021
734865a
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Dec 9, 2021
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1 change: 1 addition & 0 deletions BasicDefinitions.h
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ class Individuals;
extern SNPs ALL_SNPS;
extern Individuals ALL_SAMPLES;
extern ofstream MATCH_FILE;
map<int, ofstream*> FILE_MAP;

enum ErrorType{RECOMB=0,MI=1};
const int HET=2;
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14 changes: 14 additions & 0 deletions GERMLINE.cpp
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Expand Up @@ -7,6 +7,7 @@
using namespace std;

ofstream MATCH_FILE;
map<int, ofstream*> FILE_MAP;
size_t num_samples;
unsigned long num_matches;
SNPs ALL_SNPS;
Expand Down Expand Up @@ -45,6 +46,19 @@ void GERMLINE::mine( string params )

if ( BINARY_OUT ) MATCH_FILE.open( ( out + ".bmatch" ).c_str() , ios::binary );
else MATCH_FILE.open( ( out + ".match" ).c_str() );

// Instantiate pointers to files with append access
// we want one pointer per sample?
// num_samples incremented in Individuals::addIndividual
// This is called in PEDIndividualsExtractor which is
// called in getIndividuals
stringstream sstm;
for (int i=0;i<num_samples ;i++)
{
sstm.str("");
sstm << "match_file_" << i << ".match";
FILE_MAP[i] = new ofstream(sstm.str(), std::ofstream::out | std::ofstream::app);
}

fout << params << endl;
fout << setw(65) << setfill('-') << ' ' << endl << setfill(' ');
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45 changes: 25 additions & 20 deletions Match.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#include "Match.h"
#include "BasicDefinitions.h"

void Match::extendBack()
{
Expand Down Expand Up @@ -322,28 +323,32 @@ void Match::print( ostream& fout )
unsigned int sid[2];
sid[0] = ALL_SNPS.getSNP(snp_start).getMarkerNumber();
sid[1] = ALL_SNPS.getSNP(snp_end).getMarkerNumber();
fout.write( (char*) &pid[0] , sizeof( unsigned int ) );
fout.write( (char*) &pid[1] , sizeof( unsigned int ) );
fout.write( (char*) &sid[0] , sizeof( unsigned int ) );
fout.write( (char*) &sid[1] , sizeof( unsigned int ) );
fout.write( (char*) &dif , sizeof( int ) );
fout.write( (char*) &hom[0] , sizeof( bool ) );
fout.write( (char*) &hom[1] , sizeof( bool ) );
ofstream fout_temp = *FILE_MAP[node[0]->getID()];
fout_temp.write( (char*) &pid[0] , sizeof( unsigned int ) );
fout_temp.write( (char*) &pid[1] , sizeof( unsigned int ) );
fout_temp.write( (char*) &sid[0] , sizeof( unsigned int ) );
fout_temp.write( (char*) &sid[1] , sizeof( unsigned int ) );
// fout.write( (char*) &dif , sizeof( int ) );
// fout.write( (char*) &hom[0] , sizeof( bool ) );
// fout.write( (char*) &hom[1] , sizeof( bool ) );
} else
{
fout << node[0]->getID() << '\t';
fout << node[1]->getID() << '\t';
fout << ALL_SNPS.getSNP(snp_start).getChr() << '\t';
fout << ALL_SNPS.getSNP(snp_start).getPhysPos() << ' ';
fout << ALL_SNPS.getSNP(snp_end).getPhysPos() << '\t';
fout << ALL_SNPS.getSNP(snp_start).getSNPID() << ' ';
fout << ALL_SNPS.getSNP(snp_end).getSNPID() << '\t';
fout << ( snp_end - snp_start + 1) << '\t';
fout << setiosflags(ios::fixed) << setprecision(2) << distance << '\t';
if ( genetic ) fout << "cM" << '\t'; else fout << "MB" << '\t';
fout << dif;
for ( int n = 0 ; n < 2 ; n++ )
if ( hom[n] ) fout << '\t' << 1; else fout << '\t' << 0;
// line_elements = line.split("\t")
// return "\t".join(line_elements[:4])
ofstream fout_temp = *FILE_MAP[node[0]->getNumericID()];
fout_temp << node[0]->getID() << '\t';
fout_temp << node[1]->getID() << '\t';
fout_temp << ALL_SNPS.getSNP(snp_start).getChr() << '\t';
fout_temp << ALL_SNPS.getSNP(snp_start).getPhysPos() << ' ';
fout_temp << ALL_SNPS.getSNP(snp_end).getPhysPos() << '\t';
// fout << ALL_SNPS.getSNP(snp_start).getSNPID() << ' ';
// fout << ALL_SNPS.getSNP(snp_end).getSNPID() << '\t';
// fout << ( snp_end - snp_start + 1) << '\t';
// fout << setiosflags(ios::fixed) << setprecision(2) << distance << '\t';
// if ( genetic ) fout << "cM" << '\t'; else fout << "MB" << '\t';
// fout << dif;
// for ( int n = 0 ; n < 2 ; n++ )
// if ( hom[n] ) fout << '\t' << 1; else fout << '\t' << 0;
fout << endl;
}
num_matches++;
Expand Down