Allowed > 2^31 hits

[rsem.git] / extractRef.cpp

diff --git a/extractRef.cpp b/extractRef.cpp
index c4f24a9a079b37a25d39d6fa969ff9ac1482f3de..0a46de0950534ea4c22f3acb8f239de66ef8415f 100644 (file)
--- a/extractRef.cpp
+++ b/extractRef.cpp
@@ -86,8 +86,14 @@ bool buildTranscript(int sp, int ep) {
                int start = items[i].getStart();
                int end = items[i].getEnd();
 
-               assert(strand == items[i].getStrand());
-               assert(seqname == items[i].getSeqName());
+               if (strand != items[i].getStrand()) {
+                 fprintf(stderr, "According to the GTF file given, a transcript has exons from different orientations!\n");
+                 exit(-1);
+               }
+               if (seqname != items[i].getSeqName()) {
+                 fprintf(stderr, "According to the GTF file given, a transcript has exons on multiple chromosomes!\n");
+                 exit(-1);
+               }
 
                if (cur_e + 1 < start) {
                        if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
@@ -113,6 +119,7 @@ void parse_gtf_file(char* gtfF) {
 
        items.clear();
        while (getline(fin, line)) {
+               if (line[0] == '#') continue; // if this line is comment, jump it
                item.parse(line);
                string feature = item.getFeature();
                if (feature == "exon") {
@@ -127,14 +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);
                        }
@@ -240,7 +247,7 @@ void writeResults(char* refName) {
 }
 
 int main(int argc, char* argv[]) {
-       if (argc < 6 || (hasMappingFile = atoi(argv[4])) && argc < 7) {
+  if (argc < 6 || ((hasMappingFile = atoi(argv[4])) && argc < 7)) {
                printf("Usage: rsem-extract-reference-transcripts refName quiet gtfF hasMappingFile [mappingFile] chromosome_file_1 [chromosome_file_2 ...]\n");
                exit(-1);
        }
@@ -296,7 +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);
                }
        }