use vcfpp.h v0.4.1

Zilong-Li · Aug 7, 2024 · f331d32 · f331d32
1 parent 9836448
commit f331d32
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Showing 5 changed files with 6 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: vcfppR
 Title: Rapid Manipulation of the Variant Call Format (VCF)
-Version: 0.4.7
+Version: 0.4.8
 Authors@R: c(
     person("Zilong", "Li", , "zilong.dk@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5859-2078")),

diff --git a/R/vcf-compare.R b/R/vcf-compare.R
@@ -64,8 +64,6 @@ vcfcomp <- function(test, truth,
                     choose_random_start = FALSE,
                     return_pse_sites = FALSE,
                     ...) {
-  if((!file.exists(test)) | (!file.exists(truth)))
-    stop("file doesn't exist")
   if(is.null(bins)){
     bins <- sort(unique(c(
       c(0, 0.01 / 1000, 0.02 / 1000, 0.05 / 1000),

diff --git a/R/vcf-summary.R b/R/vcf-summary.R
@@ -45,8 +45,6 @@ vcfsummary <- function(vcffile,
                        pass = FALSE,
                        qual = 0,
                        svtype = FALSE) {
-  if(!file.exists(vcffile))
-    stop("file doesn't exist")
   if(svtype) {
     ret <- summarySVs(vcffile, region, samples, pass, qual)
   } else {

diff --git a/R/vcf-tables.R b/R/vcf-tables.R
@@ -102,8 +102,6 @@ vcftable <- function(vcffile,
                      collapse = TRUE,
                      setid = FALSE,
                      mac = 0) {
-  if(!file.exists(vcffile))
-    stop("file doesn't exist")
   snps <- FALSE
   indels <- FALSE
   svs <- FALSE

diff --git a/src/vcfpp.h b/src/vcfpp.h
@@ -2,7 +2,7 @@
  * @file        https://github.com/Zilong-Li/vcfpp/vcfpp.h
  * @author      Zilong Li
  * @email       zilong.dk@gmail.com
- * @version     v0.4.0
+ * @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);