Modified build rules for sam/libbam.a to enable parallel build

[rsem.git] / extractRef.cpp

diff --git a/extractRef.cpp b/extractRef.cpp
index 12b3222744db41cf1602890b9ae0fccfd2dfedca..da0effc70e3c3fe25925c615d30e40f2c15b55eb 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));
@@ -241,7 +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);
        }
@@ -297,7 +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);
                }
        }