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intervalfile.cpp
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intervalfile.cpp
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#include <stdio.h>
#include <string>
#include <iostream>
#include <cstdlib>
#include <fstream>
#include <set>
#include <map>
#include <algorithm>
#include <cstdlib>
#include <vector>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <limits>
#include "intervalfile.h"
using namespace std;
// qsort chromosomes
set<string> recognized_chr;
set<string> unrecognized_chr;
//vector<string> features;
int qs_struct_chr(struct GFF items[], int left, int right);
int qs_struct_chr(struct GFF items[], int left, int right)
{
register int a, b;
int x;
string tmp;
struct GFF temp;
a = left; b = right;
int a2=0;
int b2=0;
if(a2!=a || b2!=b)
{
a2=a;
b2=b;
}
x = items[(left+right)/2].chr;
do
{
while(items[a].chr<x && (a < right)) a++;
while(items[b].chr>x && (b > left)) b--;
if(a <= b)
{
temp = items[a];
items[a] = items[b];
items[b] = temp;
a++; b--;
}
} while(a <= b);
if(left < b) qs_struct_chr(items, left, b);
if(a < right) qs_struct_chr(items, a, right);
return 1;
}
void quick_struct_chr(struct GFF items[], int count);
void quick_struct_chr(struct GFF items[], int count)
{
qs_struct_chr(items,0,count-1);
}
// qsort GFFMERGE
int qs_struct_chr_merge(struct GFFMERGE items[], int left, int right);
int qs_struct_chr_merge(struct GFFMERGE items[], int left, int right)
{
register int a, b;
int x;
string tmp;
struct GFFMERGE temp;
a = left; b = right;
int a2=0;
int b2=0;
if(a2!=a || b2!=b)
{
a2=a;
b2=b;
}
x = items[(left+right)/2].chr;
do
{
while(items[a].chr<x && (a < right)) a++;
while(items[b].chr>x && (b > left)) b--;
if(a <= b)
{
temp = items[a];
items[a] = items[b];
items[b] = temp;
a++; b--;
}
} while(a <= b);
if(left < b) qs_struct_chr_merge(items, left, b);
if(a < right) qs_struct_chr_merge(items, a, right);
return 1;
}
void quick_struct_chr_merge(struct GFFMERGE items[], int count);
void quick_struct_chr_merge(struct GFFMERGE items[], int count)
{
qs_struct_chr_merge(items,0,count-1);
}
//qsort positions
int qs_struct_pos(struct GFF items[], int left, int right);
int qs_struct_pos(struct GFF items[], int left, int right)
{
register int a, b;
int x;
struct GFF temp;
a = left; b = right;
x = items[(left+right)/2].start;
do
{
while( (items[a].start < x) && (a < right)) a++;
while( (items[b].start > x) && (b > left)) b--;
if(a <= b)
{
temp = items[a];
items[a] = items[b];
items[b] = temp;
a++; b--;
}
} while(a <= b);
if(left < b) qs_struct_pos(items, left, b);
if(a < right) qs_struct_pos(items, a, right);
return 1;
}
void quick_struct_pos(struct GFF items[], int begin, int count);
void quick_struct_pos(struct GFF items[], int begin, int count)
{
qs_struct_pos(items,begin,count-1);
}
//qsort MERGE positions
int qs_struct_pos_merge(struct GFFMERGE items[], int left, int right);
int qs_struct_pos_merge(struct GFFMERGE items[], int left, int right)
{
register int a, b;
int x;
struct GFFMERGE temp;
a = left; b = right;
x = items[(left+right)/2].start;
do
{
while( (items[a].start < x) && (a < right)) a++;
while( (items[b].start > x) && (b > left)) b--;
if(a <= b)
{
temp = items[a];
items[a] = items[b];
items[b] = temp;
a++; b--;
}
} while(a <= b);
if(left < b) qs_struct_pos_merge(items, left, b);
if(a < right) qs_struct_pos_merge(items, a, right);
return 1;
}
void quick_struct_pos_merge(struct GFFMERGE items[], int begin, int count);
void quick_struct_pos_merge(struct GFFMERGE items[], int begin, int count)
{
qs_struct_pos_merge(items,begin,count-1);
}
// Check chromosome; chromosome name recognition
int guess_chr(char *str1);
int guess_chr(char *str1)
{
string tempchr=" ";
int guess=0;
tempchr.assign(str1);
if(tempchr.length()>3 && (tempchr.substr(0,3)=="CHR" || tempchr.substr(0,3)=="Chr"))
{
tempchr.assign(tempchr.substr(3,tempchr.length()));
}
if(((tempchr.length()==1 || tempchr.length()==2) && (atoi(tempchr.c_str()) > 0 && atoi(tempchr.c_str()) < 27 && isdigit(tempchr[0]))))
{
guess=atoi(tempchr.c_str());
}
// Non-autosomal chromosomes
else if(tempchr.length()==1 && (tempchr.substr(0,1)=="X" || tempchr.substr(0,1)=="x"))
{
guess=23;
}
else if(tempchr.length()==1 && (tempchr.substr(0,1)=="Y" || tempchr.substr(0,1)=="y"))
{
guess=24;
}
else if(tempchr.length()==2 && (tempchr.substr(0,2)=="XY" || tempchr.substr(0,2)=="xy"))
{
guess=25;
}
else if((tempchr.length()==2 && (tempchr.substr(0,2)=="MT" || tempchr.substr(0,2)=="mt" || tempchr.substr(0,2)=="Mt")) || (tempchr.length()==1 && (tempchr.substr(0,1)=="M" || tempchr.substr(0,1)=="m") ))
{
guess=26;
}
if(guess!=0)
{
recognized_chr.insert(tempchr);
}
else if(guess==0)
{
unrecognized_chr.insert(tempchr);
}
return guess;
}
int get_gff_data(string intervalfile, int flanking, int merging, int expandIntervals, int catIntervals, string intervalfile_format, int featurecol, struct GFFCHR * gffchr, fstream &errorfile, fstream &logfile, string outputname,int intervaleditor, int verbose);
int get_gff_data(string intervalfile, int flanking, int merging, int expandIntervals, int catIntervals, string intervalfile_format, int featurecol, struct GFFCHR * gffchr, fstream &errorfile, fstream &logfile, string outputname,int intervaleditor, int verbose)
{
int i,j,k;
int lines=0;
int chrlines=0;
int tmpchrom=0;
int cols=3;
int chrcol=0;
int startcol=1;
int endcol=2;
char *str2=NULL;
char *str3=NULL;
for(i=0; i<26; i++)
{
gffchr[i].relmapstart=0; // relative start position in *.map
gffchr[i].relmapend=0; // relative end position in *.map
gffchr[i].relmergestart=-1; // relative start position in gffmerge
gffchr[i].relmergeend=-1; // relative end position in gffmerge
gffchr[i].mergein=0;
gffchr[i].mapin=0;
}
// Fill gffchr[i],absstart/end;
char s[500000]; //First line of input file should not have more characters than this!!!!!
char s2[500000];
char c;
char *str1=NULL;
// char *str2=NULL;
//bool commentline;
bool chrfound;
string uniqtemp=" ";
string tempchr=" " ;
//char commentchar='#';
int l=0;
FILE *gff=NULL;
int chr=0;
int start=0;
int end=0;
char *feature=NULL;
char *attribute=NULL;
char *gene_id=NULL;
char *gene_name=NULL;
char *sep=NULL;
char *param=NULL;
char **mparam=NULL;
int nrparams=0;
int headerlines=0;
int tmpheaderlines=0;
vector<char*> params;
char *bf=NULL;
if(intervalfile!=" " && intervalfile_format==" ")
{
cout<<"Proceed with default parameters 'CHR'=1,'START'=2,END='3';";
cout<<"\nIf necessary, modify with INTERVAL_FORMAT CHR=\"[1-N]\";START=\"[1-N]\";END=\"[1-N]\";FEATURE=\"[1-N]\";"<<endl;
}
// commentchar='#';
chrcol=0;
startcol=1;
endcol=2;
featurecol=-9;
if(intervalfile_format!=" "){
cout << "\nInterpreting INTERVALFILE_FORMAT string "<<intervalfile_format<<"\n"<<endl;
logfile<< "\nInterpreting INTERVALFILE_FORMAT string "<<intervalfile_format<<"\n"<<endl;
bf=(char*)intervalfile_format.c_str();
str1=strtok(bf,";");
params.push_back(str1);
nrparams++;
while(str1!=NULL)
{
str1=strtok(NULL,";");
if(str1!=NULL)
{
params.push_back(str1);
nrparams++;
}
}
for(i=0; i<nrparams; i++)
{
str2=params[i];
// str2=mparam[i];
str2=strtok(str2,"=");
param=str2;
str2=strtok(NULL,"=");
str2=strtok(str2,"\"\'");
if(strcmp(param,"HEADER")==0||strcmp(param,"HEAD")==0)
{
headerlines=atoi(str2);
cout <<param<<":\t\t "<<headerlines << " headerlines expected."<<endl;
logfile <<param<<":\t\t "<<headerlines << " headerlines expected."<<endl;
}
else if(strcmp(param,"CHR")==0||strcmp(param,"CHROMOSOME")==0||strcmp(param,"CHRCOL")==0)
{
chrcol=atoi(str2)-1;
cout <<param<<":\t\t chromosome will be read from column nr. "<<chrcol+1 << "."<<endl;
logfile <<param<<":\t\t chromosome will be read from column nr. "<<chrcol+1 << "."<<endl;
}
else if(strcmp(param,"START")==0||strcmp(param,"STARTCOL")==0)
{
startcol=atoi(str2)-1;
cout <<param<<":\t\t interval start will be read from column nr. "<<startcol+1 << "."<<endl;
logfile <<param<<":\t\t interval start will be read from column nr. "<<startcol+1 << "."<<endl;
}
else if(strcmp(param,"END")==0||strcmp(param,"ENDCOL")==0)
{
endcol=atoi(str2)-1;
cout <<param<<":\t\t interval end will be read from column nr. "<<endcol+1 << "."<<endl;
logfile <<param<<":\t\t interval end will be read from column nr. "<<endcol+1 << "."<<endl;
}
else if(strcmp(param,"FEAT")==0||strcmp(param,"FEATURE")==0||strcmp(param,"FEATURECOL")==0)
{
featurecol=atoi(str2)-1;
if(featurecol>=0)
{
cout <<param<<":\t\t feature will be read from column nr. "<<featurecol+1 << "."<<endl;
logfile <<param<<":\t\t feature will be read from column nr. "<<featurecol+1 << "."<<endl;
}
else
{
cout <<"FEATURE:\t\t feature was not provided."<<endl;
logfile <<"FEATURE:\t\t feature was not provided."<<endl;
featurecol=-9;
}
}
str2=strtok(NULL,"\"");
}
}
c='0';
//check lines and columns
cout << "Opening intervalfile "<<intervalfile<<"...\n";
logfile << "Opening intervalfile "<<intervalfile<<"...\n";
int readlines=countLines(intervalfile);
lines=readlines-headerlines;
cols=countColumnsWithHeader(intervalfile,headerlines, lines);
cout << cols << " columns in " << intervalfile<<endl;
cout <<"\n"<< headerlines<<" header lines + "<<lines << " interval lines in " << intervalfile;
gff=fopen(intervalfile.c_str(),"r");
// Parameter-QC
if(intervalfile_format!=" " || cols<3){
if(cols<3 || cols > 100)
{
cout << "Invalid number of columns ("<<cols<<") in INTERVALFILE"<<endl;
logfile << "Invalid number of columns ("<<cols<<") in INTERVALFILE"<<endl;
errorfile << "Invalid number of columns ("<<cols<<") in INTERVALFILE"<<endl;
exit(1);
}
if(chrcol>=cols)
{
cout << "Chromosome column larger than number of cols!"<<endl;
logfile << "Chromosome column larger than number of cols!"<<endl;
errorfile << "Chromosome column larger than number of cols!"<<endl;
exit(1);
}
if(startcol>=cols)
{
cout << "Start column larger than number of cols!"<<endl;
logfile << "Start column larger than number of cols!"<<endl;
errorfile << "Start column larger than number of cols!"<<endl;
exit(1);
}
if(endcol>=cols)
{
cout << "End column larger than number of cols!"<<endl;
logfile << "End column larger than number of cols!"<<endl;
errorfile << "End column larger than number of cols!"<<endl;
exit(1);
}
if(featurecol!=-9 && featurecol>=cols)
{
cout << "Feature column larger than number of cols!"<<endl;
logfile << "Feature column larger than number of cols!"<<endl;
errorfile << "Feature column larger than number of cols!"<<endl;
exit(1);
}
cout<<"\n";
}
i=0;
// read intervalfile
while(!feof(gff))
{
c=fgetc(gff);
if(headerlines!=0)
{
for(tmpheaderlines=0; tmpheaderlines<headerlines; tmpheaderlines++)
{
c=fgetc(gff);
if(feof(gff)){
cout<<"File ended while reading header."<<endl;
logfile<<"File ended while reading header."<<endl;
errorfile<<"File ended while reading header."<<endl;
exit(1);
}
while(c!='\n'){
c=fgetc(gff);
if(feof(gff)){
cout<<"File ended while reading header."<<endl;
logfile<<"File ended while reading header."<<endl;
errorfile<<"File ended while reading header."<<endl;
exit(1);
}
}
lines++;
}
headerlines=0;
if(feof(gff))
{
cout<<"File unexpectedly ended."<<endl;
logfile<<"File unexpectedly ended."<<endl;
errorfile<<"File unexpectedly ended."<<endl;
exit(1);
}
}
else if(c=='\n')
{
lines++;
gffdata = (struct GFF *) realloc(gffdata, (chrlines+1) * sizeof(struct GFF));
if(featurecol<0)
{
gffdata[chrlines].feature=NULL;
}
chrfound=0;
s2[i]='\0';
i=0;
str1 = strtok(s2, "\t ");
j=0;
while(j<cols)
{
if (j==chrcol)
{
chr=guess_chr(str1);
if(chr==0)
{
break;
}
gffdata[chrlines].chr = 0;
gffdata[chrlines].chr=chr-1;
}
else if(j==startcol)
{
start=atoi(str1);
if(start==0)
{
break;
}
gffdata[chrlines].start=start;
}
else if(j==endcol)
{
end=atoi(str1);
if(end==0)
{
break;
}
gffdata[chrlines].end=end;
}
else if (featurecol>=0 && j==featurecol)
{
gffdata[chrlines].feature = NULL;
gffdata[chrlines].feature=(char *) realloc(gffdata[chrlines].feature, (strlen(str1)+ 1) * sizeof(char));
strcpy(gffdata[chrlines].feature,str1);
}
if(j<cols)
{
str1 = strtok(NULL, "\t ");
if(str1==NULL)
{
str1=(char*)"-";
}
}
if(chr!=0)
{
gffchr[chr-1].in=1;
}
j++;
}
if(chr!=0 && start!=0 && end!=0)
{
// Check Identicals
if (chrlines!=0)
{
if(gffdata[chrlines].chr==gffdata[chrlines-1].chr && gffdata[chrlines].start==gffdata[chrlines-1].start && gffdata[chrlines].end==gffdata[chrlines-1].end)
{
cout << "WARNING! known interval encountered and dismissed in line "<<lines<<" ";
cout << " chr:"<<gffdata[chrlines].chr+1<<", start:"<<gffdata[chrlines-1].start <<", end:"<<gffdata[chrlines-1].end <<"."<<endl;
logfile << "WARNING! Identical/invalid interval detected and dismissed in line "<<lines<<" ";
logfile << " chr:"<<gffdata[chrlines].chr+1<<", start:"<<gffdata[chrlines-1].start <<", end:"<<gffdata[chrlines-1].end <<"."<<endl;
errorfile << "WARNING! Identical/invalid interval detected and dismissed in line "<<lines<<" ";
errorfile << " chr:"<<gffdata[chrlines].chr+1<<", start:"<<gffdata[chrlines-1].start <<", end:"<<gffdata[chrlines-1].end <<"."<<endl;
chrlines--;
}
}
chrlines++;
}
}
else
{
s2[i++]=c;
}
} //end while
fclose(gff);
int chrqcin=0;
cout << chrlines << " accepted lines.\n" << endl;
logfile <<"\n"<< lines << " lines found in " << intervalfile << "."<<endl;
logfile << chrlines << " accepted lines.\n" << endl;
if(recognized_chr.size()!=0)
{
cout<< "Recognized chromosomes in intervalfile: ";
logfile<< "Recognized chromosomes in intervalfile: ";
for (set<string>::iterator it=recognized_chr.begin(); it!=recognized_chr.end(); it++)
{
cout << " " << *it<< " ";
logfile << " " << *it<< " ";
}
}
cout <<endl;
if(unrecognized_chr.size()!=0)
{
cout<< "\nCould not interpret element: ";
logfile<< "\nCould not interpret element: ";
logfile<< "\nWARNING: Could not interpret element: ";
for (set<string>::iterator it=unrecognized_chr.begin(); it!=unrecognized_chr.end(); it++)
{
cout << " " << *it<< " ";
logfile << " " << *it<< " ";
errorfile << " " << *it<< " ";
}
cout <<endl;
logfile <<endl;
errorfile <<endl;
}
recognized_chr.clear();
unrecognized_chr.clear();
int temppos;
int nrswitches=0;
// Positions Check
if(chrlines>2)
{
cout << "\nChecking if start and end positions of intervals are in the correct order...";
logfile << "\nChecking if start and end positions of intervals are in the correct order...";
for(i=0; i<chrlines; i++)
{
if ((gffdata[i].end-gffdata[i].start)<0)
{
temppos=gffdata[i].start;
gffdata[i].start=gffdata[i].end;
gffdata[i].end=temppos;
nrswitches++;
}
}
if(nrswitches!=0)
{
errorfile << "\nChecking if start and end positions of intervals are in the correct order...";
cout<<"\n"<<nrswitches << " start and end positions have been switched on recognized chromosomes.\n"<<endl;
errorfile<<"\n"<<nrswitches << " start and end positions have been switched on recognized chromosomes.\n"<<endl;
}
else
{
cout << " Ok!\n"<<endl;
}
}
// Check Positions, fix PAR
if(chrlines>2)
{
cout << "\nSorting chromosomes...\t";
quick_struct_chr(gffdata, chrlines);
int tmpchr=-1;
for(i = 0; i<chrlines; i++)
{
if(tmpchr!=gffdata[i].chr)
{
cout << gffdata[i].chr+1 <<" ";
tmpchr=gffdata[i].chr;
}
}
cout << "\n"<<endl;
}
i=0;
j=0;
// Find relative positions of chromosomes
for(i=1; i<chrlines; i++)
{
if(i==1)
{
gffchr[gffdata[i-1].chr].start=0;
if(gffdata[i-1].chr!=gffdata[i].chr)
{
gffchr[gffdata[i-1].chr].end=i;
}
else if(gffdata[i-1].chr==gffdata[i].chr)
{
gffchr[gffdata[i-1].chr].end=i;
}
}
else if(gffdata[i].chr!=gffdata[i-1].chr)
{
gffchr[gffdata[i].chr].start=i;
gffchr[gffdata[i-1].chr].end=i-1;
}
else if(i==chrlines-1)
{
gffchr[gffdata[i].chr].end=i;
if(gffdata[i-1].chr!=gffdata[i].chr)
{
gffchr[gffdata[i].chr].start=i;
}
}
// cout<<gffdata[i-1].start<<" " <<gffdata[i-1].end<<endl;
// cout<<gffdata[i].start<<" " <<gffdata[i].end<<endl;
}
// Print chromosome start- and endpoints
if(verbose==2 && chrlines>2)
{
cout << "Relative positions of chromosomes in interval list:"<<endl;
cout << "Chr\tfrom\tto"<<endl;
for(i=0; i<26; i++)
{
if(gffchr[i].in==1)
{
cout << i+1<<"\t"<< gffchr[i].start+1 <<"\t" << gffchr[i].end+1 <<endl;
}
}
cout <<endl;
}
// Sort according to positions
if(chrlines>2)
{
cout << "Sorting positions on chr ";
for(i=0; i< 26; i++)
{
if(gffchr[i].in==1)
{
cout << i+1<<" ";
quick_struct_pos(gffdata, gffchr[i].start, gffchr[i].end+1);
}
}
cout <<" \n" <<endl;
}
// Print chromosome spans
// cout << "Interval coverage on individual chromosomes (not counting uncovered start and end segments of chromosomes):\n"<<endl;
// cout << "Chromosome\tSpan(bp)\t\tSumIntervalLengths\t\tCoverage"<<endl;
//
// for(i=0; i<26; i++)
// {
// int intervalLengths=0;
// int intervalSpan=0;
// if(gffchr[i].in==1)
// {
// for(j=gffchr[i].start; j<gffchr[i].end+1; j++)
// {
// intervalLengths+=gffdata[j].end-gffdata[j].start+1;
// }
//
// intervalSpan=gffdata[gffchr[i].end].end - gffdata[gffchr[i].start].start + 1;
//
// if(i==24)
// {
// intervalSpan=gffdata[gffchr[i].end].end-gffdata[gffchr[i].start].start+1-(par[0].endgap-par[0].startgap+1);
// }
// cout << i+1<<"\t\t"<< intervalSpan <<"\t\t"<< intervalLengths <<"\t\t"<<(float)intervalLengths/(float)intervalSpan<<endl;
// }
// }
//
// cout <<"\n";
//
mergelines=chrlines; // Holds if there is no merging
// Check if all starts are sorted
if(chrlines>2)
{
cout << "Checking order of start positions...";
logfile << "Checking order of start positions...";
for(i=1; i<chrlines; i++)
{
gffchr[gffdata[i-1].chr].end=i-1;
if(gffdata[i-1].chr==gffdata[i].chr)
{
if(gffdata[i-1].start>gffdata[i].start)
{
cout <<"\nProblem with sorting of positions on chr "<< gffdata[i].chr+1 <<":" <<gffdata[i].start <<"-" << gffdata[i].end<<endl;
logfile <<"\nProblem with sorting of positions on chr "<< gffdata[i].chr+1 <<":" <<gffdata[i].start <<"-" << gffdata[i].end<<endl;
errorfile <<"\nProblem with sorting of positions on chr "<< gffdata[i].chr+1 <<":" <<gffdata[i].start <<"-" << gffdata[i].end<<endl;
exit(1);
}
}
}
cout<<"\n";
}
// MERGING
// Check if merging necessary
// Check if merging necessary
if(chrlines>2){
cout << "Checking if there is an overlap between intervals...";
logfile << "Checking if there is an overlap between intervals...";
}
int overlappingIntervals=0;
for(i=1; i<chrlines; i++)
{
if(gffdata[i-1].chr==gffdata[i].chr)
{
if(gffdata[i-1].end>=gffdata[i].start)
{
cout <<" Yes!\n"<<endl;
logfile <<" Yes!\n"<<endl;
overlappingIntervals=1;
break;
}
}
}
if(overlappingIntervals==0 && chrlines>2)
{
cout <<" No!\n"<<endl;
logfile <<" No!\n"<<endl;
}
if(merging==1 && overlappingIntervals==0)
{
cout << "MERGE_INTERVALS is not necessary! There is no overlap between intervals."<<endl;
logfile << "MERGE_INTERVALS is not necessary! There is no overlap between intervals."<<endl;
}
else if(merging==1 && overlappingIntervals==1)
{
cout << "Merging intervalfile intervals...\n"<<endl;
logfile << "Merging intervalfile intervals...\n"<<endl;
// Intervals are extended to the limits of their overlap; their number is NOT reduced
int overlapBins=0;
char *tmpfeature=NULL;
int oldbin=0;
int newchr=1;
int stepback=1;
int i2=0;
string tmpstr=" ";
// Number of lines in future merged struct
mergelines=0;
i2=0; // future mergelines;
for(i=0; i<chrlines; i++)
{
gfftmp = (struct GFFMERGE *) realloc(gfftmp, (i2+1) * sizeof(struct GFFMERGE));
gfftmp[i2].chr=gffdata[i].chr;
gfftmp[i2].end=gffdata[i].end;
gfftmp[i2].start=gffdata[i].start;
if(featurecol>=0)
{
gfftmp[i2].feature = NULL;
gfftmp[i2].feature = (char*) realloc(gfftmp[i2].feature, (strlen(gffdata[i].feature)+ 1) * sizeof(char));
gfftmp[i2].feature = gffdata[i].feature;
}
merged=0;
mergeend=gffdata[i].end;
mergestart=gffdata[i].start;
if(featurecol>=0)
{
tmpfeature=NULL;
tmpfeature=gffdata[i].feature;
}
while(gffdata[i].chr==gffdata[i+1].chr && i<chrlines-1 && gffdata[i+1].start <= mergeend)
{
merged=1;
if(featurecol>=0)
{
// tmpfeature=gffdata[i+1].feature;
sprintf(tmpfeature,"%s,%s",tmpfeature,gffdata[i+1].feature);
}
if(gffdata[i+1].end >= mergeend)
{
mergeend=gffdata[i+1].end;
}
gfftmp[i2].end=mergeend;
i++;
}
if(merged==1)
{
if(featurecol>=0)
{
gfftmp[i2].feature = NULL;
gfftmp[i2].feature = (char*) realloc(gfftmp[i2].feature, (strlen(tmpfeature)+ 1) * sizeof(char));
gfftmp[i2].feature = tmpfeature;
}
}
merged=0;
i2++;
}
mergelines=i2;
cout <<"After MERGE_INTERVALFILE_INTERVALS: "<<mergelines<<" intervals obtained from "<<chrlines<<" intervals."<<endl;
logfile <<"After MERGE_INTERVALFILE_INTERVALS: "<<mergelines<<" intervals obtained from "<<chrlines<<" intervals."<<endl;
}
cout <<"\nResulting intervals: "<<mergelines<<endl;
logfile <<"\nResulting intervals: "<<mergelines<<endl;
gffmerge = (struct GFFMERGE *) realloc(gffmerge, (mergelines) * sizeof(struct GFFMERGE));
if(merging==1 && overlappingIntervals ==1)
{
for(i=0; i<mergelines; i++)
{
gffmerge[i].chr=gfftmp[i].chr;
gffmerge[i].start=gfftmp[i].start;
gffmerge[i].end=gfftmp[i].end;
if(featurecol>=0)
{
gffmerge[i].feature = NULL;
gffmerge[i].feature = (char*) realloc(gffmerge[i].feature, (strlen(gfftmp[i].feature)+ 1) * sizeof(char));
// strcpy( gffmerge[i].feature, gfftmp[i].feature);
gffmerge[i].feature = gfftmp[i].feature;
}
}
overlappingIntervals=0;
}
// else if( overlappingIntervals == 0)
else
{
for(i=0; i<mergelines; i++)
{
gffmerge[i].chr=gffdata[i].chr;
gffmerge[i].start=gffdata[i].start;
gffmerge[i].end=gffdata[i].end;
if(featurecol>=0)
{
gffmerge[i].feature = NULL;
gffmerge[i].feature = (char*) realloc(gffmerge[i].feature, (strlen(gffdata[i].feature)+ 1) * sizeof(char));
strcpy(gffmerge[i].feature,gffdata[i].feature);
}
}
}
free(gffdata);
i=0;
// Merging finished
// Find NEW relative positions of chromosomes
for(i=1; i<mergelines; i++)
{
if(i==1)
{
gffchr[gffmerge[i-1].chr].start=0;
if(gffmerge[i-1].chr!=gffmerge[i].chr)
{
gffchr[gffmerge[i-1].chr].end=i;
}
else if(gffmerge[i-1].chr==gffmerge[i].chr)
{
gffchr[gffmerge[i-1].chr].end=i-1;
}
}
else if(gffmerge[i].chr!=gffmerge[i-1].chr)
{