From d7604b4648e8a3297de5fa66764ffb1150a29f3b Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Sun, 7 Apr 2024 09:07:03 +0200
Subject: [PATCH] fix asan issues. safe to use writeLine and addLine

---
 test/Makefile       | 10 +++++-----
 test/bcf-writer.cpp | 11 +----------
 vcfpp.h             | 23 +++++++++++------------
 3 files changed, 17 insertions(+), 27 deletions(-)

diff --git a/test/Makefile b/test/Makefile
index 1f4fa9d..c09983b 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -1,12 +1,12 @@
-# detect OS architecture and add flags
-CXX      = g++
-# CXXFLAGS = -std=c++11 -Wall -g -fsanitize=address
-CXXFLAGS = -std=c++11 -Wall
 HTSINC   = /usr/local/include
 HTSLIB   = /usr/local/lib
+# detect OS architecture and add flags
+CXX      = g++
+CXXFLAGS = -std=c++11 -Wall -fsanitize=address
+# CXXFLAGS = -std=c++11 -Wall
 LDFLAGS  =  -L$(HTSLIB) -Wl,-rpath,$(HTSLIB)
 LIBS     = -lhts -lz -lm -lbz2 -llzma -lcurl -lpthread
-INC      = -I. -I..
+INC      = -I. -I.. -I${HTSINC}
 
 OBJS = test-main.o bcf-variant.o bcf-reader.o bcf-writer.o example.o
 
diff --git a/test/bcf-writer.cpp b/test/bcf-writer.cpp
index 58d9e4a..8f68655 100644
--- a/test/bcf-writer.cpp
+++ b/test/bcf-writer.cpp
@@ -28,16 +28,7 @@ TEST_CASE("Write BCF with custome header and variants", "[bcf-writer]")
     bw.header.addContig("chr20");
     bw.header.addSample("NA12878");
     bw.writeLine("chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGT\t1|0");
-}
-
-TEST_CASE("Write VCF with custome header and variants", "[bcf-writer]")
-{
-    BcfWriter bw("test.vcf", "VCF4.3");
-    bw.header.addFORMAT("GT", "1", "String", "Genotype");
-    bw.header.addINFO("AF", "A", "Float", "Estimated allele frequency in the range (0,1)");
-    bw.header.addContig("chr20");
-    bw.header.addSample("NA12878");
-    bw.writeLine("chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGT\t1|0");
+    bw.close();
 }
 
 
diff --git a/vcfpp.h b/vcfpp.h
index 5fbbc26..d865f8a 100644
--- a/vcfpp.h
+++ b/vcfpp.h
@@ -2,7 +2,7 @@
  * @file        https://github.com/Zilong-Li/vcfpp/vcfpp.h
  * @author      Zilong Li
  * @email       zilong.dk@gmail.com
- * @version     v0.3.4
+ * @version     v0.3.6
  * @breif       a single C++ file for manipulating VCF
  * Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file.
  ******************************************************************************/
@@ -876,10 +876,10 @@ class BcfRecord
     /** @brief add one variant record from given string*/
     void addLineFromString(const std::string & vcfline)
     {
-        std::vector<char> str(vcfline.begin(), vcfline.end());
-        str.push_back('\0'); // don't forget string has no \0;
-        kstring_t s = {vcfline.length(), vcfline.length(), &str[0]}; // kstring
-        ret = vcf_parse(&s, header.hdr, line.get());
+        kstring_t s = {0, 0, NULL};
+        kputsn(vcfline.c_str(), vcfline.length(), &s);
+        ret = vcf_parse1(&s, header.hdr, line.get());
+        free(s.s);
         if(ret > 0) throw std::runtime_error("error parsing: " + vcfline + "\n");
         if(line->errcode == BCF_ERR_CTG_UNDEF)
         {
@@ -892,7 +892,6 @@ class BcfRecord
             if(ret < 0) throw std::runtime_error("error adding contig " + contig + " to header.\n");
             ret = bcf_hdr_sync(header.hdr);
         }
-        free(s.s);
     }
 
     /** @brief if all samples have non missing values for the tag in FORMAT */
@@ -1434,7 +1433,7 @@ class BcfReader
                 int slen = tbx_itr_next(fp.get(), tidx, itr, &s);
                 if(slen > 0)
                 {
-                    ret = vcf_parse(&s, r.header.hdr, r.line.get()); // ret > 0, error
+                    ret = vcf_parse1(&s, r.header.hdr, r.line.get()); // ret > 0, error
                     bcf_unpack(r.line.get(), BCF_UN_ALL);
                 }
                 return (ret <= 0) && (slen > 0);
@@ -1574,14 +1573,14 @@ class BcfWriter
         if(header.hdr == NULL) throw std::runtime_error("couldn't copy the header from another vcf.\n");
     }
 
-    /// write a string to a vcf line
+    /// copy a string to a vcf line
     void writeLine(const std::string & vcfline)
     {
         if(!isHeaderWritten && !writeHeader()) throw std::runtime_error("could not write header\n");
-        std::vector<char> str(vcfline.begin(), vcfline.end());
-        str.push_back('\0'); // don't forget string has no \0;
-        kstring_t s = {vcfline.length(), vcfline.length(), &str[0]}; // kstring
-        ret = vcf_parse(&s, header.hdr, b.get());
+        kstring_t s = {0, 0, NULL};
+        kputsn(vcfline.c_str(), vcfline.length(), &s);
+        ret = vcf_parse1(&s, header.hdr, b.get());
+        free(s.s);
         if(ret > 0) throw std::runtime_error("error parsing: " + vcfline + "\n");
         if(b->errcode == BCF_ERR_CTG_UNDEF)
         {