@@ -1,9 +1,9 @@

 # Generated by roxygen2: do not edit by hand

 export(get_lineage_report)

+export(is_gff3)

 export(lineagespot)

 export(lineagespot_hits)

-export(list_gff3)

 export(list_input)

 export(list_vcf)

 export(merge_vcf)

@@ -66,7 +66,7 @@ list_vcf <- function(vcf_fls = NULL,

 }

-#' list_gff3

+#' is_gff3

 #'

 #' @description

 #' Identify whether a file is in GFF3 format.

@@ -84,8 +84,8 @@ list_vcf <- function(vcf_fls = NULL,

 #' gff3_path <- system.file("extdata", "NC_045512.2_annot.gff3",

 #'   package = "lineagespot"

 #' )

-#' list_gff3(gff3_path)

-list_gff3 <- function(file) {

+#' is_gff3(gff3_path)

+is_gff3 <- function(file) {

   if (is.null(file)) {

     stop(c(

       "Please provide a valid GFF3 file",

@@ -101,7 +101,7 @@ list_gff3 <- function(file) {

     stop("Please give path of only one GFF3 file.")

   }

-  res <- str_detect(file, "gff3")

+  res <- str_detect(file, ".gff3$")

   return(res)

 }

@@ -149,10 +149,12 @@ list_input <- function(vcf_fls = NULL,

     stop("No VCF is found. Please insert valid input files.")

   }

-  if (list_gff3(gff3_path) == FALSE) {

+  if (is_gff3(gff3_path) == FALSE) {

     stop("No valid gff3 was given. Please insert path of valid gff3.")

   }

   return(vcf_fls)

 }

+

+

similarity index 81%

rename from man/list_gff3.Rd

rename to man/is_gff3.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/input_checking.R

-\name{list_gff3}

-\alias{list_gff3}

-\title{list_gff3}

+\name{is_gff3}

+\alias{is_gff3}

+\title{is_gff3}

 \usage{

-list_gff3(file)

+is_gff3(file)

 }

 \arguments{

 \item{file}{Path to GFF3 file.}

@@ -20,5 +20,5 @@ Identify whether a file is in GFF3 format.

 gff3_path <- system.file("extdata", "NC_045512.2_annot.gff3",

   package = "lineagespot"

 )

-list_gff3(gff3_path)

+is_gff3(gff3_path)

 }

@@ -30,9 +30,9 @@ test_that('Input file is vcf',{

 })

 test_that('Input file is gff3',{

-    expect_true(list_gff3(system.file("extdata","NC_045512.2_annot.gff3",

+    expect_true(is_gff3(system.file("extdata","NC_045512.2_annot.gff3",

                                     package = "lineagespot")))

-    expect_false(list_gff3(system.file("extdata","vcf-files",

+    expect_false(is_gff3(system.file("extdata","vcf-files",

                                     "SampleA_freebayes_ann.vcf",

                                     package = "lineagespot")))

 })