X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=extractRef.cpp;h=fb7d3ecb586d36e586d8698a9f4c94bc0ec4cc46;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hp=1a56cc15e8c615f02e14c7cd15f4e8c787e5a172;hpb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980;p=rsem.git

diff --git a/extractRef.cpp b/extractRef.cpp
index 1a56cc1..fb7d3ec 100644
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -260,7 +260,6 @@ int main(int argc, char* argv[]) {
 
 	ifstream fin;
 	string line, gseq, seqname;
-	void* pt;
 
 	chrvec.clear();
 
@@ -270,31 +269,31 @@ int main(int argc, char* argv[]) {
 	for (int i = start; i < argc; i++) {
 		fin.open(argv[i]);
 		if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[i]); exit(-1); }
-		pt = getline(fin, line);
-		while (pt != 0 && line[0] == '>') {
+		getline(fin, line);
+		while ((fin) && (line[0] == '>')) {
 			istringstream strin(line.substr(1));
 			strin>>seqname;
 
 			gseq = "";
-		    while((pt = getline(fin, line)) && line[0] != '>') {
-		    	gseq += line;
-		    }
-
-		    size_t len = gseq.length();
-		    assert(len > 0);
-		    for (size_t j = 0; j < len; j++) gseq[j] = check(gseq[j]);
-
-		    iter = sn2tr.find(seqname);
-		    if (iter == sn2tr.end()) continue;
-
-		    chrvec.push_back(ChrInfo(seqname, len));
-
-		    vector<int>& vec = iter->second;
-		    int s = vec.size();
-		    for (int j = 0; j < s; j++) {
-		    	assert(vec[j] > 0 && vec[j] <= M);
-		    	transcripts.getTranscriptAt(vec[j]).extractSeq(gseq, seqs[vec[j]]);
-		    }
+			while((getline(fin, line)) && (line[0] != '>')) {
+			  gseq += line;
+			}
+
+			size_t len = gseq.length();
+			assert(len > 0);
+			for (size_t j = 0; j < len; j++) gseq[j] = check(gseq[j]);
+			
+			iter = sn2tr.find(seqname);
+			if (iter == sn2tr.end()) continue;
+			
+			chrvec.push_back(ChrInfo(seqname, len));
+			
+			vector<int>& vec = iter->second;
+			int s = vec.size();
+			for (int j = 0; j < s; j++) {
+			  assert(vec[j] > 0 && vec[j] <= M);
+			  transcripts.getTranscriptAt(vec[j]).extractSeq(gseq, seqs[vec[j]]);
+			}
 		}
 		fin.close();