From 2f18c2c1abac71fb28c286ab444941f01bd6224d Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Mon, 9 Oct 2017 15:55:00 +0200
Subject: [PATCH] main.cpp: Add snprintf code in similar code section

Introduce snprintf & LINEBUFFSIZE in similar section for
'single-read alignments'. This should make the code a bit
cleaner.
---
 main.cpp | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/main.cpp b/main.cpp
index 0f0b22d..9c252a2 100644
--- a/main.cpp
+++ b/main.cpp
@@ -564,12 +564,20 @@ void RunProcess(void) {
         }
 
 		if(param.out_sam&&param.sam_header) {
-			char _ch[1000];
+			char _ch[LINEBUFFSIZE];
+			int ret_len;
 			for(bit32_t i=0;i<ref.total_num;i++) {
-				sprintf(_ch,"@SQ\tSN:%s\tLN:%u\n",ref.title[i<<1].name.c_str(),ref.title[i<<1].size);
+				ret_len=snprintf(_ch,LINEBUFFSIZE,"@SQ\tSN:%s\tLN:%u\n",ref.title[i<<1].name.c_str(),ref.title[i<<1].size);
+				if (ret_len>=LINEBUFFSIZE) {
+					cerr<<"Buffer error, output was truncated (increase LINEBUFFSIZE in main.cpp and recompile)."<<endl;
+				}
 				_str.append(_ch);
 			}
-			sprintf(_ch,"@PG\tID:BSMAP\tVN:%s\tCL:\"%s\"\n",version,command_line.c_str()); _str.append(_ch);
+			ret_len=snprintf(_ch,LINEBUFFSIZE,"@PG\tID:BSMAP\tVN:%s\tCL:\"%s\"\n",version,command_line.c_str());
+			if (ret_len>=LINEBUFFSIZE) {
+				cerr<<"Buffer error, output was truncated (increase LINEBUFFSIZE in main.cpp and recompile)."<<endl;
+			}
+			_str.append(_ch);
 			if(param.stdout) cout<< _str;
 			else if(param.pipe_out) fwrite(_str.c_str(),1,_str.size(),pout);
 			else fout<<_str;