Merge pull request #10 from DEploid-dev/change_submodule_path

Change submodule path

.Rbuildignore

@@ -4,13 +4,33 @@
 LICENSE
 .github
 \*\.o
-src/vcf/vcfReader.o
-src/vcf/gzstream/gzstream.o
-src/vcf/txtReader.o
-src/vcf/variantIndex.o
-src/vcf/vcfReaderDebug.o
-DEploid.utils/libs/DEploid.utils.so
 \*\.png
 \*\.pdf
 DEploid-vcf-lib
 codecov.yml
+
+
+# submodule
+vcf/src/gzstream/version
+src/vcf/.git
+src/vcf/.ci/
+src/vcf/.circleci/
+src/vcf/.github/
+src/vcf/.gitignore
+src/vcf/Brewfile
+src/vcf/COPYING
+src/vcf/CPPLINT.cfg
+src/vcf/Makefile.am
+src/vcf/README.md
+src/vcf/bootstrap
+src/vcf/configure.ac
+src/vcf/coverage/
+src/vcf/data/
+src/vcf/main.cpp
+src/vcf/tests/
+src/vcf/version
+src/vcf/src/gzstream/gzstream.o
+src/vcf/src/txtReader.o
+src/vcf/src/variantIndex.o
+src/vcf/src/vcfReader.o
+src/vcf/src/vcfReaderDebug.o

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

@@ -32,6 +32,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pr-commands.yaml

@@ -19,6 +19,8 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -18,6 +18,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - uses: r-lib/actions/setup-r@v2
         with:

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "DEploid-vcf-lib"]
-	path = DEploid-vcf-lib
+	path = src/vcf
 	url = https://github.com/DEploid-dev/DEploid-vcf-lib

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DEploid.utils
 Title: 'DEploid' Data Analysis and Results Interpretation  
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7566-2787")),

R/errorAnalysis.r

@@ -173,7 +173,9 @@ dEploidOutError_3 <- function(h.pair, h.pair.true, rel.cost.switch = 2, do.plot
 
   dropTimes <- sum(diff(drop.strain) != 0)
   dropError <- sum(drop.strain != 0)
-  cat("\nDecoding gives:\nNo. switches:\t", n.s - dropTimes, "\nNo. GT errs:\t", n.gt, "\nNo. Drop errs:\t", dropError, "\n")
+  message(paste0("\nDecoding gives:\nNo. switches:\t", n.s - dropTimes,
+                 "\nNo. GT errs:\t", n.gt,
+                 "\nNo. Drop errs:\t", dropError, "\n"))
   return(list(
     switchError = n.s - dropTimes,
     mutError = n.gt,
@@ -299,7 +301,10 @@ dEploidOutError_2 <- function(h.pair, h.pair.true, rel.cost.switch = 2, do.plot
   #    definite.switch = sum(!changed.permn.at %in% changed.k.eff.at)
   dropTimes <- sum(diff(drop.strain) != 0) # length(changed.k.eff.at)
   dropError <- sum(drop.strain != 0)
-  cat("\nDecoding gives:\nNo. switches:\t", n.s - dropTimes, "\nNo. GT errs:\t", n.gt, "\nNo. Drop switches", dropTimes, "\nNo. Drop errs:\t", dropError, "\n")
+  message(paste0("\nDecoding gives:\nNo. switches:\t",n.s - dropTimes,
+                 "\nNo. GT errs:\t", n.gt,
+                 "\nNo. Drop switches", dropTimes,
+                 "\nNo. Drop errs:\t", dropError, "\n"))
 
 
   hap.pair.true.idx <- array(unlist(possible.permn[op]), c(2, length(op)))

R/plotting.R

@@ -132,7 +132,7 @@ plot_total_coverage <- function(ref, alt, chroms, cex.lab = 1, cex.main = 1, cex
 }
 
 
-fun_dataExplore <- function(coverage, PLAF, prefix = "", pdfBool, threshold = 0.995, window.size = 10) {
+fun_dataExplore <- function(coverage, PLAF, prefix = tempdir(), pdfBool, threshold = 0.995, window.size = 10) {
   #    PLAF = plafInfo$PLAF
   ref <- coverage$refCount
   alt <- coverage$altCount
@@ -189,7 +189,7 @@ fun_dataExplore <- function(coverage, PLAF, prefix = "", pdfBool, threshold = 0.
 }
 
 
-fun_interpretDEploid_best <- function(coverage, PLAF, dEploidPrefix, prefix = "", exclude, pdfBool) {
+fun_interpretDEploid_best <- function(coverage, PLAF, dEploidPrefix, prefix = tempdir(), exclude, pdfBool) {
   ref <- coverage$refCount
   alt <- coverage$altCount
 
@@ -243,7 +243,7 @@ fun_interpretDEploid_best <- function(coverage, PLAF, dEploidPrefix, prefix = ""
 }
 
 
-fun_interpretDEploid_1 <- function(coverage, PLAF, dEploidPrefix, prefix = "", exclude, pdfBool) {
+fun_interpretDEploid_1 <- function(coverage, PLAF, dEploidPrefix, prefix = tempdir(), exclude, pdfBool) {
   #    PLAF = plafInfo$PLAF
   ref <- coverage$refCount
   alt <- coverage$altCount
@@ -375,7 +375,7 @@ plot_wsaf_vs_index <- function(coverage, expWSAF = c(), expWSAFChrom = c(), excl
 }
 
 
-fun_interpretDEploid_2 <- function(coverage, dEploidPrefix, prefix = "", exclude, pdfBool, ringBool = FALSE, dEploid_v = "classic") {
+fun_interpretDEploid_2 <- function(coverage, dEploidPrefix, prefix = tempdir(), exclude, pdfBool, ringBool = FALSE, dEploid_v = "classic") {
   dEploidOutput <- fun_dEploidPrefix(dEploidPrefix, dEploid_v)
   if (dEploid_v == "classic") {
     tmpProp <- read.table(dEploidOutput$propFileName, header = F)
@@ -464,7 +464,7 @@ plot_postProb_ofCase <- function(inPrefix, outPrefix, case, strainNumber, pdfBoo
 }
 
 
-fun_interpretDEploid_3 <- function(inPrefix, outPrefix = "", pdfBool, inbreeding = FALSE) {
+fun_interpretDEploid_3 <- function(inPrefix, outPrefix = tempdir(), pdfBool, inbreeding = FALSE) {
   strainI <- 0
   while (file.exists(paste(inPrefix, ".single", strainI, sep = ""))) {
     plot_postProb_ofCase(inPrefix, outPrefix, paste("single", strainI, sep = ""), strainI, pdfBool)
@@ -476,7 +476,7 @@ fun_interpretDEploid_3 <- function(inPrefix, outPrefix = "", pdfBool, inbreeding
 }
 
 
-fun_interpretDEploid_4 <- function(inPrefix, outPrefix = "", pdfBool) {
+fun_interpretDEploid_4 <- function(inPrefix, outPrefix = tempdir(), pdfBool) {
   inFile <- paste(inPrefix, ".ibd.probs", sep = "")
   if (!file.exists(inFile)) {
     warning("In file not exist")
@@ -508,7 +508,7 @@ fun_interpretDEploid_4 <- function(inPrefix, outPrefix = "", pdfBool) {
 }
 
 
-fun_interpretDEploid_3_ring <- function(inPrefix, outPrefix = "", pdfBool, inbreeding = FALSE, coverage, exclude, ringDecreasingOrder, trackHeight = 0.8, transformP = FALSE) {
+fun_interpretDEploid_3_ring <- function(inPrefix, outPrefix = tempdir(), pdfBool, inbreeding = FALSE, coverage, exclude, ringDecreasingOrder, trackHeight = 0.8, transformP = FALSE) {
   if (pdfBool == TRUE) {
     cexSize <- 3
     if (inbreeding) {
@@ -639,7 +639,7 @@ plot_ibd_change <- function(changeAt, titlePrefix, nFigures) {
 }
 
 
-# fun_interpretDEploid_4 <- function(inPrefix, outPrefix = "", pdfBool){
+# fun_interpretDEploid_4 <- function(inPrefix, outPrefix = tempdir(), pdfBool){
 #    fileName = paste(inPrefix, ".extra", sep = "")
 #    if ( file.exists(fileName) ){
 #        obj = read.table(fileName , header=T)

src/Makevars.win

@@ -1,11 +1,11 @@
 OBJECTS.vcfr = rvcf.o \
   RcppExports.o \
-  vcf/txtReader.o \
-  vcf/variantIndex.o \
-  vcf/vcfReader.o \
-  vcf/gzstream/gzstream.o \
-  vcf/vcfReaderDebug.o
+  vcf/src/txtReader.o \
+  vcf/src/variantIndex.o \
+  vcf/src/vcfReader.o \
+  vcf/src/gzstream/gzstream.o \
+  vcf/src/vcfReaderDebug.o
 
 OBJECTS = $(OBJECTS.vcfr)
-PKG_CXXFLAGS = -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS
+PKG_CXXFLAGS = -I/usr/share/R/include/ -Ivcf/src/ -Ivcf/src/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS
 PKG_LIBS = -lz

src/rvcf.cpp

@@ -1,5 +1,5 @@
 #include <Rcpp.h>
-#include "vcf/vcfReader.hpp"
+#include "vcf/src/vcfReader.hpp"
 
 using namespace Rcpp;