From c23d96eeb065020cf53dfa54969d0260a5d65dc8 Mon Sep 17 00:00:00 2001
From: jlanej <jlanej@gmail.com>
Date: Fri, 29 Mar 2024 13:40:35 -0500
Subject: [PATCH] initial file stub

---
 .gitignore     |  2 +-
 Dockerfile     |  9 +++++++++
 bamRUtils.R    | 29 +++++++++++++++++++++++++++++
 longReadPlot.R |  3 +++
 4 files changed, 42 insertions(+), 1 deletion(-)
 create mode 100644 bamRUtils.R
 create mode 100644 longReadPlot.R

diff --git a/.gitignore b/.gitignore
index e75435c..cc7ff3a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
 # History files
 .Rhistory
 .Rapp.history
-
+*.Rproj
 # Session Data files
 .RData
 .RDataTmp
diff --git a/Dockerfile b/Dockerfile
index 5d41ea8..aa34328 100644
--- a/Dockerfile
+++ b/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"]
+
diff --git a/bamRUtils.R b/bamRUtils.R
new file mode 100644
index 0000000..4f7f2d3
--- /dev/null
+++ b/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)
+}
diff --git a/longReadPlot.R b/longReadPlot.R
new file mode 100644
index 0000000..3450a83
--- /dev/null
+++ b/longReadPlot.R
@@ -0,0 +1,3 @@
+library(optparse)
+source("bamRUtils.R")
+print("hi")
\ No newline at end of file