## ----setup, include = FALSE---------------------------------------------------
library(vcfheader)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "centre"
)

## ----eval = FALSE-------------------------------------------------------------
#  input <- parse_vcf_header("file.vcf")
#  
#  vcfheader(
#    input,
#    file = "file_report.html"
#  )

## ----echo = FALSE, out.width = "100%"-----------------------------------------
knitr::include_graphics("simple_vcfheader_screenshot1.png")
knitr::include_graphics("simple_vcfheader_screenshot2.png")

## -----------------------------------------------------------------------------
simple_vcf <- system.file("extdata", "simple.vcf", package = "vcfheader")
sv_vcf <- system.file("extdata", "sv44.vcf", package = "vcfheader")

basename(simple_vcf)
basename(sv_vcf)

## -----------------------------------------------------------------------------
hdr_lines <- read_vcf_header(simple_vcf)
head(hdr_lines, 5)

## -----------------------------------------------------------------------------
hdr <- parse_vcf_header(simple_vcf)
hdr

## -----------------------------------------------------------------------------
names(hdr)

## -----------------------------------------------------------------------------
file_meta <- hdr$file
file_meta$input_path <- basename(file_meta$input_path)
file_meta

## -----------------------------------------------------------------------------
hdr$samples

## -----------------------------------------------------------------------------
hdr$info[, c("ID", "Number", "Type", "Description")]

## -----------------------------------------------------------------------------
hdr$format[, c("ID", "Number", "Type", "Description")]

## -----------------------------------------------------------------------------
hdr$warnings
hdr$errors

## -----------------------------------------------------------------------------
hdr$file$caller_guess

## -----------------------------------------------------------------------------
sv_hdr <- parse_vcf_header(sv_vcf)
sv_hdr

## -----------------------------------------------------------------------------
sv_hdr$contigs[, intersect(c("ID", "length", "assembly", "md5"), names(sv_hdr$contigs)), drop = FALSE]

## -----------------------------------------------------------------------------
sv_hdr$alt[, c("ID", "Description")]

## -----------------------------------------------------------------------------
sv_hdr$info[, c("ID", "Number", "Type", "Description")]

## -----------------------------------------------------------------------------

hdr <- parse_vcf_header("file.vcf")

out_file <- "file_report.html"

vcfheader(
  hdr,
  file = out_file
)

file.exists(out_file)
basename(out_file)

## ----eval = FALSE-------------------------------------------------------------
#  vcfheader(hdr)

## -----------------------------------------------------------------------------
example_report <- system.file(
  "extdata",
  "simple_vcfheader.html",
  package = "vcfheader"
)


basename(example_report)
file.exists(example_report)