From 49079e241d33c4b9bc5eb92aed3f2da741f52a71 Mon Sep 17 00:00:00 2001
From: gkarthik <xraydiffraction@gmail.com>
Date: Fri, 7 Jun 2024 18:58:26 -0700
Subject: [PATCH] Ignore empty lines that are usually present at end of file

---
 src/parse_gff.cpp | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/parse_gff.cpp b/src/parse_gff.cpp
index b78a7db9..f9cdcc8a 100644
--- a/src/parse_gff.cpp
+++ b/src/parse_gff.cpp
@@ -37,18 +37,18 @@ gff3_feature::gff3_feature(std::string line) {
     }
     ctr++;
   }
-  if (ctr < 9) std::cout << "GFF file is not in GFF3 file format!" << std::endl;
+  if (ctr < 9) std::cerr << "GFF file is not in GFF3 file format!" << std::endl;
   line_stream.clear();
 }
 
 int gff3_feature::print() {
-  std::cout << seqid << "\t" << source << "\t" << type << "\t" << start << "\t"
+  std::cerr << seqid << "\t" << source << "\t" << type << "\t" << start << "\t"
             << end << "\t" << score << "\t" << strand << "\t" << phase << "\t";
   std::map<std::string, std::string>::iterator it;
   for (it = attributes.begin(); it != attributes.end(); it++) {
-    std::cout << it->first << ": " << it->second << "; ";
+    std::cerr << it->first << ": " << it->second << "; ";
   }
-  std::cout << std::endl;
+  std::cerr << std::endl;
   return 0;
 }
 
@@ -131,16 +131,22 @@ gff3::gff3(std::string path) {
 int gff3::read_file(std::string path) {
   std::ifstream fin = std::ifstream(path);
   if (!fin) {
-    std::cout << "GFF file does not exist at " << path << std::endl;
+    std::cerr << "GFF file does not exist at " << path << std::endl;
     return -1;
   }
   std::string line;
   while (std::getline(fin, line)) {
     if (line[0] == '#')  // Avoid comments in GFF file
       continue;
-    features.push_back(gff3_feature(line));
+    if(!line.empty())
+      features.push_back(gff3_feature(line));
   }
-  this->is_empty = false;
+  if(!features.empty()){
+    this->is_empty = false;
+  } else {
+    std::cerr << "GFF file is empty!" << std::endl;
+  }
+
   return 0;
 }