X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=extractRef.cpp;h=0a46de0950534ea4c22f3acb8f239de66ef8415f;hp=693af6635ae9df85006dcc7b991ee5d2e497bed8;hb=9eef8b58056b7cdaad1b4bdb2b2904d9fc0ff430;hpb=37513308b7557ae65899e59df8e43b5dec90da5c

diff --git a/extractRef.cpp b/extractRef.cpp
index 693af66..0a46de0 100644
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -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);
  			}
@@ -303,7 +303,9 @@ int main(int argc, char* argv[]) {
 
 	for (int i = 1; i <= M; i++) {
 		if (seqs[i] == "") {
-			fprintf(stderr, "%s's sequence is empty! You must provide all chromosome files of transcripts which are presented in the .gtf file!\n", transcripts.getTranscriptAt(i).getTranscriptID().c_str());
+			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());
 			exit(-1);
 		}
 	}