v0.5.0

Zilong-Li · Sep 22, 2024 · f3e5ce5 · f3e5ce5
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# vcfppR 0.5.0
+* upgrade `vcfpp.h` to v0.5.1
+* add `bcfreader$updateSamples()` function
+* `vcfcomp`: can take `vcftable` object as input
+* `vcfcomp`: defaults changed `setid=FALSE`
+* bug fix
+
+
 # vcfppR 0.4.6
 * add `vcfplot` function
 * fix bug in `vcftable` when FORMAT has unaligned list 

diff --git a/README.Rmd b/README.Rmd
@@ -88,14 +88,14 @@ Want to investigate the concordance between two VCF files? `vcfcomp` is the util
 ```{r r2}
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
                stats = "r2", region = "chr21:1-5100000", 
-               formats = c("GT","GT"))
+               formats = c("GT","GT"), setid = TRUE)
 par(mar=c(5,5,2,2), cex.lab = 2)
 vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 ```
 
 ```{r pse}
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
-               stats = "pse",
+               stats = "pse", setid = TRUE,
                region = "chr21:5000000-5500000",
                samples = "HG00673,NA10840",
                return_pse_sites = TRUE)
@@ -124,9 +124,25 @@ vcfplot(res, main = "Structure Variant Counts", col = 1:7)
 
 ## R API of vcfpp.h
 
-There are two classes i.e. ***vcfreader*** and ***vcfwriter*** offering the full R-bindings of vcfpp.h. Check out the examples in the [tests](tests/testthat) folder or refer to the manual.
+There are two classes i.e. ***vcfreader*** and ***vcfwriter*** offering the full
+R-bindings of vcfpp.h. Check out the examples in the [tests](tests/testthat)
+folder or refer to the manual, e.g. `?vcfppR::vcfreader`.
 
 ```r
-?vcfppR::vcfreader
+library(testthat)
+test_that("can change samples name and set genotypes for single sample", {
+  br <- vcfreader$new(svfile, "", "HG00096")
+  br$variant()
+  br$genotypes(F)
+  br$setGenotypes(c(1L,1L))
+  outfile <- paste0(tempfile(), ".vcf.gz")
+  br$output(outfile)
+  br$updateSamples("ZZZZZ")
+  br$write()
+  br$close()
+  vcf <- vcftable(outfile)
+  expect_true(vcf$gt==2)
+  expect_true(vcf$samples=="ZZZZZ")
+})
 ```
 
diff --git a/README.md b/README.md
@@ -97,7 +97,7 @@ to calculate the genotype correlation between the test and the truth.
 ``` r
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
                stats = "r2", region = "chr21:1-5100000", 
-               formats = c("GT","GT"))
+               formats = c("GT","GT"), setid = TRUE)
 par(mar=c(5,5,2,2), cex.lab = 2)
 vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 ```
@@ -106,7 +106,7 @@ vcfplot(res, col = 2,cex = 2, lwd = 3, type = "b")
 
 ``` r
 res <- vcfcomp(test = rawvcf, truth = phasedvcf,
-               stats = "pse",
+               stats = "pse", setid = TRUE,
                region = "chr21:5000000-5500000",
                samples = "HG00673,NA10840",
                return_pse_sites = TRUE)
@@ -146,8 +146,23 @@ vcfplot(res, main = "Structure Variant Counts", col = 1:7)
 
 There are two classes i.e. ***vcfreader*** and ***vcfwriter*** offering
 the full R-bindings of vcfpp.h. Check out the examples in the
-[tests](tests/testthat) folder or refer to the manual.
+[tests](tests/testthat) folder or refer to the manual,
+e.g. `?vcfppR::vcfreader`.
 
 ``` r
-?vcfppR::vcfreader
+library(testthat)
+test_that("can change samples name and set genotypes for single sample", {
+  br <- vcfreader$new(svfile, "", "HG00096")
+  br$variant()
+  br$genotypes(F)
+  br$setGenotypes(c(1L,1L))
+  outfile <- paste0(tempfile(), ".vcf.gz")
+  br$output(outfile)
+  br$updateSamples("ZZZZZ")
+  br$write()
+  br$close()
+  vcf <- vcftable(outfile)
+  expect_true(vcf$gt==2)
+  expect_true(vcf$samples=="ZZZZZ")
+})
 ```
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/PULL_REQUEST_TEMPLATE.html b/docs/PULL_REQUEST_TEMPLATE.html
diff --git a/docs/articles/concordance-of-two-vcf-files.html b/docs/articles/concordance-of-two-vcf-files.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   concordance-of-two-vcf-files: concordance-of-two-vcf-files.html
-last_built: 2024-05-24T08:40Z
+last_built: 2024-09-22T08:53Z
 
diff --git a/docs/reference/index.html b/docs/reference/index.html