initial file stub

.gitignore

@@ -1,7 +1,7 @@
 # History files
 .Rhistory
 .Rapp.history
-
+*.Rproj
 # Session Data files
 .RData
 .RDataTmp

Dockerfile

@@ -1 +1,10 @@
 FROM r-base
+
+RUN R -e "install.packages('optparse',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages('Rsamtools',dependencies=TRUE, repos='http://cran.rstudio.com/')"
+ENV BASE=/app/
+
+WORKDIR ${BASE}
+COPY ./ ${BASE}
+CMD ["Rscript", "longReadPlot.R"]
+

bamRUtils.R

@@ -0,0 +1,29 @@
+require(Rsamtools)
+
+
+.unlist <- function (x)
+{
+  ## do.call(c, ...) coerces factor to integer, which is undesired
+  x1 <- x[[1L]]
+  if (is.factor(x1)) {
+    structure(unlist(x), class = "factor", levels = levels(x1))
+  } else {
+    do.call(c, x)
+  }
+}
+
+convertBam <- function(bam, param) {
+  bam <- unname(bam) # names not useful in unlisted result
+  elts <- setNames(bamWhat(param), bamWhat(param))
+  lst <- lapply(elts, function(elt)
+    .unlist(lapply(bam, "[[", elt)))
+  lst = lst[lengths(lst) != 0]
+  df <- do.call("data.frame", bam)
+  return(df)
+}
+
+loadBam <- function(bamFile, param) {
+  bam = scanBam(bamFile, param = param)
+  bam = convertBam(bam = bam, param = param)
+  return(bam)
+}

longReadPlot.R

@@ -0,0 +1,3 @@
+library(optparse)
+source("bamRUtils.R")
+print("hi")