Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / extractRef.cpp

diff --git a/extractRef.cpp b/extractRef.cpp
index 3173d6517c1fccd6edcf03fa15502b64faadb28d..1a56cc15e8c615f02e14c7cd15f4e8c787e5a172 100644 (file)
--- 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);
                        }
@@ -304,9 +304,8 @@ int main(int argc, char* argv[]) {
        for (int i = 1; i <= M; i++) {
                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());
+                       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.getSeqName().c_str());
                        exit(-1);
                }
        }