Added .gitignore to ignore built files

[rsem.git] / GTFItem.h

diff --git a/GTFItem.h b/GTFItem.h
index a908375c9296ca1ba9ce0717969b11e30bffd109..e0499be9139ab226a1643aea47e379e92af275f4 100644 (file)
--- a/GTFItem.h
+++ b/GTFItem.h
@@ -80,8 +80,10 @@ public:
                        }
                }
 
-               my_assert(find_gene_id, line, "Cannot find gene_id!");
-               my_assert(find_transcript_id, line, "Cannot find transcript_id!");
+               my_assert(feature != "exon" || find_gene_id, line, "Cannot find gene_id!");
+               my_assert(feature != "exon" || find_transcript_id, line, "Cannot find transcript_id!");
+               if (!find_gene_id && feature != "exon") { printf("Warning: line \" %s \" does not contain a gene_id attribute! Since this line will not be used for reference construction, it is skipped. But if you think this GTF file is corrupted, you should find a complelete GTF file instead and rebuild the reference.\n", line.c_str()); }
+               if (!find_transcript_id && feature != "exon") { printf("Warning: line \" %s \" does not contain a transcript_id attribute! Since this line will not be used for reference construction, it is skipped. But if you think this GTF file is corrupted, you should find a complelete GTF file instead and rebuild the reference.\n", line.c_str()); }
        }
 
        std::string getSeqName() { return seqname; }