add mxsize argument to cmalign

Author: brendanf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: inferrnal
 Title: Interface to Call Programs from Infernal RNA Covariance Model Package
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: 
     person(given = "Brendan",
            family = "Furneaux",

NEWS.md

@@ -1,3 +1,7 @@
+# inferrnal 0.99.3
+
+* Added `mxsize` argument to `cmalign` to change the maximum matrix size.
+
 # inferrnal 0.99.2
 
 * Added convenience functions `cm_5_8S()`, `sample_rRNA_fasta()`,

R/inferrnal.R

@@ -200,6 +200,11 @@ cmsearch <- function(cm, seq, glocal = TRUE, alignment, cpu) {
 #'        See \href{http://eddylab.org/infernal/}{Infernal} documentation for
 #'        more information.
 #' @param cpu (\code{integer} scalar) The number of cpus to use.
+#' @param mxsize (\code{double} scalar) The maximum DP matrix size, in Mb.
+#'        Maximum potential memory usage is approximately cpu*mxsize, although
+#'        this is usually not realized.
+#'        See \href{http://eddylab.org/infernal/}{Infernal} documentation for
+#'        more information.
 #'
 #' @return the aligned sequences, as returned by
 #'     \code{\link{read_stockholm_msa}}.
@@ -213,7 +218,7 @@ cmsearch <- function(cm, seq, glocal = TRUE, alignment, cpu) {
 #'     # also works if the fasta file has already been loaded
 #'     unaln <- Biostrings::readRNAStringSet(unaln)
 #'     cmalign(cm, unaln, cpu = 1)
-cmalign <- function(cmfile, seq, glocal = TRUE, cpu) {
+cmalign <- function(cmfile, seq, glocal = TRUE, cpu = NULL, mxsize = NULL) {
     assertthat::assert_that(assertthat::is.readable(cmfile),
                             assertthat::is.flag(glocal))
     args <- "cmalign"
@@ -222,6 +227,12 @@ cmalign <- function(cmfile, seq, glocal = TRUE, cpu) {
         assertthat::assert_that(assertthat::is.count(cpu))
         args <- c(args, "--cpu", cpu)
     }
+    if (!missing(mxsize)) {
+        assertthat::assert_that(
+            assertthat::is.number(mxsize),
+            mxsize > 0)
+        args <- c(args, "--mxsize", mxsize)
+    }
 
     seqfile <- NULL
     if (assertthat::is.string(seq) && file.exists(seq)) {