update

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pr-commands.yaml

@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -36,5 +36,6 @@ vignettes/*.pdf
 rsconnect/
 
 # DEploid compile
+*o
 *bak
 .Rproj.user

DESCRIPTION

@@ -5,7 +5,20 @@ Authors@R:
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: Apache License (>= 2)
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
+Depends:
+    R (>= 3.1.0)
+Imports:
+    Rcpp (>= 0.11.2),
+    scales (>= 0.4.0),
+    plotly (>= 4.7.1),
+    magrittr (>= 1.5),
+    rmarkdown(>= 1.6),
+    htmlwidgets (>= 1.0)
+Suggests:
+    knitr,
+    testthat (>= 0.9.0)
+VignetteBuilder: knitr
+LinkingTo: Rcpp
 RoxygenNote: 7.3.2
+Encoding: UTF-8
+Date: 2024-11-18

NAMESPACE

@@ -4,9 +4,13 @@ export(computeObsWSAF)
 export(extractCoverageFromTxt)
 export(extractCoverageFromVcf)
 export(extractPLAF)
+export(extractVcf)
 export(haplotypePainter)
 export(histWSAF)
 export(plotAltVsRef)
 export(plotObsExpWSAF)
 export(plotProportions)
 export(plotWSAFvsPLAF)
+importFrom(Rcpp,evalCpp)
+importFrom(scales,alpha)
+useDynLib(DEploid.utils, .registration = TRUE)

R/RcppExports.R

@@ -0,0 +1,33 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' @title Extract VCF information
+#'
+#' @description Extract VCF information
+#'
+#' @param filename VCF file name.
+#'
+#' @seealso
+#' \itemize{
+#'   \item \code{extractCoverageFromVcf}
+#'   \item \code{extractCoverageFromTxt}
+#' }
+#'
+#' @return A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.
+#' \itemize{
+#'   \item \code{CHROM} SNP chromosomes.
+#'   \item \code{POS} SNP positions.
+#'   \item \code{refCount} reference allele count.
+#'   \item \code{altCount} alternative allele count.
+#' }
+#'
+#' @export
+#'
+#' @examples
+#' vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
+#' vcf = extractVcf(vcfFile, "PG0390-C")
+#'
+extractVcf <- function(filename, samplename) {
+    .Call(`_DEploid_utils_extractVcf`, filename, samplename)
+}
+

R/deploid_utils.R

@@ -0,0 +1,28 @@
+#' @keywords internal
+"_PACKAGE"
+
+#' Deconvolute Mixed Genomes with Unknown Proportions
+#'
+#' Traditional phasing programs are limited to diploid organisms.
+#' Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
+#' (MCMC) approaches, and builds a generic framework that allows haplotype
+#' searches in a multiple infection setting. This package is primarily developed
+#' as part of #' the Pf3k project, which is a global collaboration using the
+#' latest sequencing technologies to provide a high-resolution view of natural
+#' variation in the malaria parasite Plasmodium falciparum. Parasite DNA are
+#' extracted from patient blood sample, which often contains more than one
+#' parasite strain, with unknown proportions. This package is used for
+#' deconvoluting mixed haplotypes, #' and reporting the mixture proportions from
+#' each sample.
+#'
+#' @author
+#' Joe Zhu
+#'
+#' Maintainer: Joe Zhu \email{[email protected]}
+#'
+#' @name DEploid.utils-package
+#'
+#' @importFrom Rcpp evalCpp
+#' @importFrom scales alpha
+#' @useDynLib DEploid.utils, .registration = TRUE
+NULL