X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parseIt.cpp;h=8620432c2840140561451c211208b560b7e48363;hb=97554bbac838f2ed578d81f98e421dac0669e74e;hp=55dd954d3d1e2059911987ed5a8521748b16e9a1;hpb=58f823f5be6dfbe00896fc44ac3aac5e881e9c5c;p=rsem.git

diff --git a/parseIt.cpp b/parseIt.cpp
index 55dd954..8620432 100644
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -13,8 +13,6 @@
 #include "utils.h"
 
 #include "GroupInfo.h"
-
-#include "Transcript.h"
 #include "Transcripts.h"
 
 #include "SingleRead.h"
@@ -96,6 +94,9 @@ void parseIt(SamParser *parser) {
 			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);
@@ -127,6 +128,9 @@ void parseIt(SamParser *parser) {
 	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);
@@ -220,9 +224,11 @@ int main(int argc, char* argv[]) {
 	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();