#include "utils.h"
#include "GroupInfo.h"
-
-#include "Transcript.h"
#include "Transcripts.h"
#include "SingleRead.h"
if (record_val >= 0) {
record_read.write(n_os, cat[record_val]);
++N[record_val];
+ }
+ // flush out previous read's hits if the read is alignable reads
+ if (record_val == 1) {
hits.updateRI();
nHits += hits.getNHits();
nMulti += hits.calcNumGeneMultiReads(gi);
if (record_val >= 0) {
record_read.write(n_os, cat[record_val]);
++N[record_val];
+ }
+
+ if (record_val == 1) {
hits.updateRI();
nHits += hits.getNHits();
nMulti += hits.calcNumGeneMultiReads(gi);
fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
fout<<nHits<<" "<<read_type<<endl;
+ fout<<"0\t"<<N[0]<<endl;
for (iter = counter.begin(); iter != counter.end(); iter++) {
fout<<iter->first<<'\t'<<iter->second<<endl;
}
+ fout<<"Inf\t"<<N[2]<<endl;
fout.close();
release();