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#ifndef STRINGTIE_MERGE_H_
#define STRINGTIE_MERGE_H_
#include "GStr.h"
#include "GList.hh"
#include "rlink.h"
extern GStr tmp_path;
extern GStr cram_ref;
extern bool keepTempFiles;
struct TInputRecord {
GSamRecord* brec;
int fidx; //index in files and readers
bool operator<(TInputRecord& o) {
//decreasing location sort
GSamRecord& r1=*brec;
GSamRecord& r2=*(o.brec);
//int refcmp=strcmp(r1.refName(),r2.refName());
int refcmp=mergeMode ? strcmp(r1.refName(),r2.refName()) : r1.refId()-r2.refId();
if (refcmp==0) {
//higher coords first
if (r1.start!=r2.start)
return (r1.start>r2.start);
else {
if (r1.end!=r2.end)
return (r1.end>r2.end);
else if (fidx==o.fidx)
return (strcmp(r1.name(), r2.name())>0);
else return fidx>o.fidx;
}
}
else { //use header order
return (refcmp>0);
}
}
bool operator==(TInputRecord& o) {
GSamRecord& r1=*brec;
GSamRecord& r2=*(o.brec);
return ( strcmp(r1.refName(),r2.refName())==0 && r1.start==r2.start && r1.end==r2.end
&& fidx==o.fidx && strcmp(r1.name(),r2.name())==0);
}
TInputRecord(GSamRecord* b=NULL, int i=0):brec(b),fidx(i) {}
~TInputRecord() {
delete brec;
}
};
struct TInputFiles {
protected:
TInputRecord* crec;
GStr convert2BAM(GStr& gtf, int idx);
public:
GPVec<GSamReader> readers;
GVec<GStr> files; //same order
GVec<GStr> tmpfiles; //all the temp files created by this
GList<TInputRecord> recs; //next record for each
TInputFiles():crec(NULL), readers(true), files(), tmpfiles(),
recs(true, true, true) { }
void Add(const char* fn);
int count() { return files.Count(); }
int start(); //open all files, load 1 record from each
GSamRecord* next();
void stop(); //
};
#endif /* STRINGTIE_MERGE_H_ */
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