Fix crash reported in #26

src/Exception.h

@@ -42,7 +42,7 @@ inline void log_error(const char* s) {
 #endif
 
 inline void REPORT(const char* x) { 
-    REprintf("Report '%s' to [email protected]\n", x ); 
+    REprintf("Report '%s' at https://github.com/zhanxw/seqminer\n", x ); 
 }
 
 inline void FATAL(const char* x) {

src/FileIO.cpp

@@ -11,7 +11,7 @@ AbstractFileReader* AbstractFileReader::open(const char* fileName) {
 #ifdef _USE_KNETFILE
   if (strstr(fileName, "ftp://") == fileName || strstr(fileName, "http://") == fileName) {
     fr = new KnetFileReader(fileName);
-    REprintf("open knetfile %s\n", fileName);
+    REprintf("Open knetfile %s:%d: [ %s ]\n", __FILE__, __LINE__, fileName);
     return fr;
   }
 #endif

src/FileIO.h

@@ -266,6 +266,9 @@ class KnetFileReader : public AbstractFileReader {
   // check eof
   bool isEof() {
     // this is always false, as we don't know the exact file size
+    if (!this->fp) { // probably files are not openned
+      return true;
+    }
     return bgzf_check_EOF(this->fp);
   }
   // open

src/VCFInputFile.cpp

@@ -16,14 +16,18 @@ void VCFInputFile::rewriteVCFHeader() {
     s += '\t';
     s += people[i]->getName();
   }
-  this->header[this->header.size()-1] = s;
+  if (this->header.size()) {
+    this->header[this->header.size()-1] = s;
+  } else {
+    REprintf("[ERROR] Cannot rewriteVCFHeader() at %s:%d", __FILE__, __LINE__);
+  }
 }
 
 void VCFInputFile::setRangeMode() {
   if (mode == VCF_LINE_MODE) {
     this->tabixReader = new TabixReader(this->fileName);
     if (!this->tabixReader->good()) {
-      REprintf( "[ERROR] Cannot read VCF by range, please check your have index (or create one use tabix).\nQuitting...");
+      REprintf("[ERROR] Cannot read VCF by range, please check your have index (or create one use tabix).\nQuitting...");
       //abort();
       return;
     } else {