diff htseq_count_render.R @ 2:db9da9716914 draft

add r-dt

--- a/htseq_count_render.R	Tue Mar 06 17:38:58 2018 -0500
+++ b/htseq_count_render.R	Wed Mar 07 00:12:55 2018 -0500
@@ -10,6 +10,7 @@
 
 library(getopt)
 library(rmarkdown)
+library(htmltools)
 #------------------------------------------------
 
 
@@ -21,15 +22,16 @@
 
 spec_matrix = as.matrix(
   data.frame(stringsAsFactors=FALSE,
-              long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_f", "X_r",
-                             "X_S", "X_a", "X_T", "X_i", "X_I", "X_m"),
-             short_flags = c("e", "o", "d", "s", "t", "f", "r", "S", "a", "T",
-                             "i", "I", "m"),
-     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+              long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_A", "X_B", "X_G",
+                             "X_f", "X_r", "X_S", "X_a", "X_T", "X_i", "X_m", "X_c"),
+             short_flags = c("e", "o", "d", "s", "t", "A", "B", "G", "f", "r", "S",
+                             "a", "T", "i", "m", "c"),
+     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
+                             1L, 1L, 1L),
          data_type_flags = c("character", "character", "character", "character",
-                             "character", "character", "character",
+                             "character", "character", "character", "character",
                              "character", "character", "character", "character",
-                             "character", "character")
+                             "character", "character", "character", "character")
   )
 )
 opt = getopt(spec_matrix)