throw exception when file not existing

readme.org

@@ -6,16 +6,19 @@
 [[https://github.com/Zilong-Li/vcfpp/releases/latest][https://img.shields.io/github/v/release/Zilong-Li/vcfpp.svg]]
 [[https://img.shields.io/github/license/Zilong-Li/vcfpp?style=plastic.svg]]
 
-This project introduces vcfpp (vcf plus plus), a single C++ file as interface to the basic =htslib=, which can be easily included in a C++ program
-for scripting high-performance genomic analyses.
+This project introduces vcfpp (vcf plus plus), a single C++ file as interface to
+the basic =htslib=, which can be easily included in a C++ program for scripting
+high-performance genomic analyses. Check out [[https://github.com/Zilong-Li/vcfppR][vcfppR]] as an example of how vcfpp.h
+can facilitate rapidly writing high-performance R package.
 
 Features:
 - single file to be easily included and compiled
 - easy and safe [[https://zilongli.org/proj/vcfpp/index.html][API]] to use.
 - objects are RAII. no worry about allocate and free memory.
-- has the full functionalities of the =htslib=, eg. supports of compressed VCF/BCF and URL link as filename.
+- the full functionalities of =htslib=, e.g. supports of compressed VCF/BCF and URL link as filename.
 - compatible with C++11 and later
 
+
 * Table of Contents :TOC:QUOTE:
 #+BEGIN_QUOTE
 - [[#installation][Installation]]
@@ -93,7 +96,7 @@ value =-9= into account for downstream analysis.
 
 ** Writing VCF
 
-There are many ways in vcfpp for writing the VCF/BCF file.
+There are many ways for writing the VCF/BCF file.
 
 *** Use an empty template
 
@@ -110,13 +113,13 @@ for (auto& s : {"id01", "id02", "id03"}) bw.header.addSample(s); // add 3 sample
 bw.writeLine("chr20\t2006060\trs146931526\tG\tC\t100\tPASS\tAF=0.000998403\tGT\t1|0\t1|1\t0|0");
 #+end_src
 
-*** Use another VCF as template
+*** Use an existing VCF as template
 
-In this example, we first read VCF file
-=test/test-vcf-read.vcf.gz=. Secondly, we construct an empty variant record
-and update the record with the input VCF. Thirdly, we construct a
-BcfWriter object using the meta data in the header of the input VCF,
-writing out the header and the modified variant record.
+In this example, we first read VCF file =test/test-vcf-read.vcf.gz=. Second,
+we construct an empty variant record and update the record with the input
+VCF. Third, we construct a BcfWriter object using the meta data in the
+header of the input VCF, writing out the header and the modified variant
+record.
 
 #+begin_src C++
 BcfReader br("test/test-vcf-read.vcf.gz");

test/Makefile

@@ -2,8 +2,7 @@ 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 -g
+CXXFLAGS = -std=c++11 -Wall -g -O2 -fsanitize=address
 LDFLAGS  =  -L$(HTSLIB) -Wl,-rpath,$(HTSLIB)
 LIBS     = -lhts -lz -lm -lbz2 -llzma -lcurl -lpthread
 INC      = -I. -I.. -I${HTSINC}

test/bcf-reader.cpp

@@ -142,3 +142,11 @@ TEST_CASE("parse EV in vcf - vector<string>", "[bcf-reader]")
     REQUIRE(ev[0]=="RD");
     REQUIRE(ev[1]=="SR,PE");
 }
+
+TEST_CASE("throw error when file is not valid", "[bcf-reader]")
+{
+    BcfReader br;
+    CHECK_THROWS(br.open("no-test-GL.vcf.gz"));
+    BcfReader bw;
+    CHECK_THROWS(bw.open("ff://no-access.vcf.gz"));
+}

tools/vcf2beagle.cpp

@@ -50,7 +50,7 @@ int main(int argc, char * argv[])
     vector<double> out;
     while(vcf.getNextVariant(var))
     {
-        if(!var.isSNP()) continue;
+        // if(!var.isSNP()) continue;
         if(tag == "PL")
         {
             var.getFORMAT("PL", pl); // try get PL values

vcfpp.h

@@ -2,7 +2,7 @@
  * @file        https://github.com/Zilong-Li/vcfpp/vcfpp.h
  * @author      Zilong Li
  * @email       [email protected]
- * @version     v0.4.0
+ * @version     v0.4.1
  * @breif       a single C++ file for manipulating VCF
  * Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file.
  ******************************************************************************/
@@ -1519,6 +1519,7 @@ class BcfReader
     {
         fname = file;
         fp = std::shared_ptr<htsFile>(hts_open(file.c_str(), "r"), htsFile_close());
+        if(!fp) throw std::invalid_argument("I/O error: input file is invalid");
         header.hdr = bcf_hdr_read(fp.get());
         nsamples = bcf_hdr_nsamples(header.hdr);
         SamplesName = header.getSamples();
@@ -1710,6 +1711,7 @@ class BcfWriter
     {
         auto mode = getMode(fname, "w");
         fp = std::shared_ptr<htsFile>(hts_open(fname.c_str(), mode.c_str()), htsFile_close());
+        if(!fp) throw std::invalid_argument("I/O error: input file is invalid");
     }
 
     /**
@@ -1724,6 +1726,7 @@ class BcfWriter
     void open(const std::string & fname, const std::string & mode)
     {
         fp = std::shared_ptr<htsFile>(hts_open(fname.c_str(), mode.c_str()), htsFile_close());
+        if(!fp) throw std::invalid_argument("I/O error: input file is invalid");
     }
 
     /// close the BcfWriter object.
@@ -1751,6 +1754,7 @@ class BcfWriter
     void copyHeader(const std::string & vcffile)
     {
         htsFile * fp2 = hts_open(vcffile.c_str(), "r");
+        if(!fp2) throw std::invalid_argument("I/O error: input file is invalid");
         header.hdr = bcf_hdr_read(fp2);
         hts_close(fp2);
         initalHeader(header);