X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=extractRef.cpp;h=fb7d3ecb586d36e586d8698a9f4c94bc0ec4cc46;hb=dbcf1cfb8ad1086c21d64e249f012809403e7ddc;hp=da0effc70e3c3fe25925c615d30e40f2c15b55eb;hpb=64cbcf77f3d0a6d8dea12d4c2a6500399d9bd2a2;p=rsem.git

diff --git a/extractRef.cpp b/extractRef.cpp
index da0effc..fb7d3ec 100644
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -50,24 +50,24 @@ map<string, string> mi_table; // mapping info table
 map<string, string>::iterator mi_iter; //mapping info table's iterator
 
 void loadMappingInfo(char* mappingF) {
-  ifstream fin(mappingF);
-  string line, key, value;
-
-  if (!fin.is_open()) {
-	  fprintf(stderr, "Cannot open %s! It may not exist.\n", mappingF);
-	  exit(-1);
-  }
-
-  mi_table.clear();
-  while (getline(fin, line)) {
-    line = cleanStr(line);
-    if (line[0] == '#') continue;
-    istringstream strin(line);
-    strin>>value>>key;
-    mi_table[key] = value;
-  }
-
-  fin.close();
+	ifstream fin(mappingF);
+	string line, key, value;
+
+	if (!fin.is_open()) {
+		fprintf(stderr, "Cannot open %s! It may not exist.\n", mappingF);
+		exit(-1);
+	}
+
+	mi_table.clear();
+	while (getline(fin, line)) {
+		line = cleanStr(line);
+		if (line[0] == '#') continue;
+		istringstream strin(line);
+		strin>>value>>key;
+		mi_table[key] = value;
+	}
+
+	fin.close();
 }
 
 bool buildTranscript(int sp, int ep) {
@@ -134,14 +134,14 @@ void parse_gtf_file(char* gtfF) {
  			else {
  		 		if (hasMappingFile) {
  		 			tid = item.getTranscriptID();
- 		 		    mi_iter = mi_table.find(tid);
- 		 		    if (mi_iter == mi_table.end()) {
- 		 		    	fprintf(stderr, "Mapping Info is not correct, cannot find %s's gene_id!\n", tid.c_str());
- 		 		    	exit(-1);
- 		 		    }
- 		 		    //assert(iter != table.end());
- 		 		    gid = mi_iter->second;
- 		 		    item.setGeneID(gid);
+					mi_iter = mi_table.find(tid);
+					if (mi_iter == mi_table.end()) {
+					  fprintf(stderr, "Mapping Info is not correct, cannot find %s's gene_id!\n", tid.c_str());
+					  exit(-1);
+					}
+					//assert(iter != table.end());
+					gid = mi_iter->second;
+					item.setGeneID(gid);
  		 		}
  				items.push_back(item);
  			}
@@ -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();
 
@@ -305,7 +304,7 @@ int main(int argc, char* argv[]) {
 		if (seqs[i] == "") {
 			const Transcript& transcript = transcripts.getTranscriptAt(i);
 			fprintf(stderr, "Cannot extract transcript %s's sequence from chromosome %s, whose information might not be provided! Please check if the chromosome directory is set correctly or the list of chromosome files is complete.\n", \
-					transcript.getTranscriptID().c_str(), transcript.getGeneID().c_str());
+					transcript.getTranscriptID().c_str(), transcript.getSeqName().c_str());
 			exit(-1);
 		}
 	}