update comments and description to CRAN

DESCRIPTION

@@ -7,7 +7,7 @@ Authors@R: c(
     person("Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng",  role = "cph",
            comment = "Authors of included htslib library")
            )
-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 variant call format (VCF) file. Thus, this package is built upon the 'vcfpp.h' for rapid variant processing of the compressed or uncompressed VCF/BCF file.
+Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF/BCF files. Explore a range of powerful features for efficient VCF data manipulation.
 Encoding: UTF-8
 Depends: R (>= 3.6.0)
 Roxygen: list(markdown = TRUE)

README.Rmd

@@ -27,7 +27,7 @@ The vcfppR package implements various useful functions for manipulating the VCF/
 You can install the development version of vcfppR with the system dependencies of `libcurl`.
 
 ``` r
-## install.package("vcfppR")
+## install.package("vcfppR") ## from CRAN
 devtools::install_github("Zilong-Li/vcfppR")
 ```
 
@@ -92,7 +92,7 @@ This example shows how to summarize complex structure variants discovered by GAT
 
 ```r
 svfile <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz"
-res <- vcfsummary(svfile, svtype = TRUE)
+sv <- vcfsummary(svfile, svtype = TRUE)
 str(sv)
 allsvs <- sv$summary[-1]
 bar <- barplot(allsvs, ylim = c(0, 1.1*max(allsvs)),

README.md

@@ -19,7 +19,7 @@ You can install the development version of vcfppR with the system
 dependencies of `libcurl`.
 
 ``` r
-## install.package("vcfppR")
+## install.package("vcfppR") ## from CRAN
 devtools::install_github("Zilong-Li/vcfppR")
 ```
 
@@ -96,7 +96,7 @@ discovered by GATK-SV.
 
 ``` r
 svfile <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz"
-res <- vcfsummary(svfile, svtype = TRUE)
+sv <- vcfsummary(svfile, svtype = TRUE)
 str(sv)
 allsvs <- sv$summary[-1]
 bar <- barplot(allsvs, ylim = c(0, 1.1*max(allsvs)),

cran-comments.md

@@ -2,5 +2,9 @@ Fix the following issues.
 
 1. Removed the redundant "in R" in the title.
 2. Wrote 'C++', 'htslib' 'vcfpp.h' in single quotes
-3. Updated the .Rd files by adding \value for exported methods and classes
+3. Updated the .Rd files by adding \value and \examples for exported methods and classes
 4. Added the authors of htslib as 'cph' in ‘Authors@R’ 
+
+Comments about documenting the C++ class:
+
+I've documented each method of the C++ class by using a nested structure inside the \section(Fields), which is the only way I found that can document the C++ class by doxygen2 automatically.