verbose message

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: vcfppR
-Title: Rapid Manipulation of The VCF/BCF Format in R
+Title: Rapid Manipulation of the Variant Call Format (VCF) in R
 Version: 0.3.5
 Authors@R: 
     person("Zilong", "Li", , "[email protected]", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-5859-2078"))
-Description: The https://github.com/Zilong-Li/vcfpp is an easy-to-use C++ API of htslib, offering the full functionalities as the htslib to manipulate the VCF/BCF file. Thus, this package is built upon the vcfpp.h to provide rapid genomic variant analyses on the VCF/BCF file in R.
+Description: The <https://github.com/Zilong-Li/vcfpp> is an easy-to-use C++ API of htslib, offering the full functionalities as the htslib to manipulate the VCF/BCF file. Thus, this package is built upon the vcfpp.h to provide rapid variant processing with the variant call format in R.
 Encoding: UTF-8
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE)

R/vcf-tables.R

@@ -101,6 +101,7 @@ vcftable <- function(vcffile, region = "", samples = "-", vartype = "all", forma
   res <- NULL
   if(format == "GT") {
     res <- tableGT(vcffile, region, samples, "GT", ids, qual, pass, info, snps, indels, multiallelics, multisnps)
+    if(length(res$gt)==0) return(res)
     res[[10]] <- do.call("rbind", res[[10]])
     n <- ncol(res$gt)
     ploidy <- n / length(res$samples)
@@ -116,3 +117,4 @@ vcftable <- function(vcffile, region = "", samples = "-", vartype = "all", forma
   }
   return(res)
 }
+

README.Rmd

@@ -43,11 +43,11 @@ In addtion to two classes for R-bindings of vcfpp.h, there are some useful funct
 
 ## Read VCF as tabular data in R
 
-This example shows how to read only SNP variants with FILTER="PASS" and GT format in the VCF/BCF into R tables:
+This example shows how to read only SNP variants with genotypes in the VCF/BCF into R tables:
 ```r
 library(vcfppR)
 vcffile <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr21.filtered.SNV_INDEL_SV_phased_panel.vcf.gz"
-res <- vcftable(vcffile, "chr21:1-5100000", vartype = "snps", pass = TRUE)
+res <- vcftable(vcffile, "chr21:1-5100000", vartype = "snps")
 str(res)
 ```
 

src/vcfpp-read.cpp

@@ -177,6 +177,7 @@ List tableFormat(std::string vcffile, std::string region, std::string samples, s
             filter.push_back(var.FILTER());
             if (INFO) info.push_back(var.INFO());
         }
+        Rcout << "there is no " << format << " in the FORMAT\n";
         return List::create(Named("samples") = vcf.header.getSamples(), Named("chr") = chr,
                             Named("pos") = pos, Named("id") = id, Named("ref") = ref,
                             Named("alt") = alt, Named("qual") = qual, Named("filter") = filter,

tests/testthat/test-vcfpp-table.R

@@ -4,7 +4,7 @@ library(testthat)
 vcffile <- system.file("extdata", "raw.gt.vcf.gz", package="vcfppR")
 
 test_that("extract GT for all SNPs", {
-  res <- vcftable(vcffile, vartype = "snps")
+  res <- vcftable(vcffile, vartype = "snps", format = "AA")
   ## if all are SNPs and ALT!="."
   expect_identical(sum(res$alt!=""), length(res$alt))
 })
@@ -16,4 +16,3 @@ test_that("extract GT for variant with ID=chr21:5030516:G:A", {
   expect_equal(res$alt, "A")
 })
 
-