new readEDS code updates to make

thelovelab · Aug 7, 2019 · c7f4fe4 · c7f4fe4
1 parent 0943b3d
commit c7f4fe4
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Showing 4 changed files with 8 additions and 21 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: tximport
-Version: 1.13.11
+Version: 1.13.12
 Title: Import and summarize transcript-level estimates for transcript- and
        gene-level analysis
 Description: Imports transcript-level abundance, estimated counts and

diff --git a/NEWS b/NEWS
@@ -1,9 +1,9 @@
-CHANGES IN VERSION 1.13.11
+CHANGES IN VERSION 1.13.12
 --------------------------
 
     o Alevin count and inferential variance can be imported now 
       ~40x faster for large number of cells, leveraging C++ code
-      from the fishpond package (>= 1.1.17).
+      from the fishpond package (>= 1.1.18).
 
 CHANGES IN VERSION 1.13.8
 -------------------------

diff --git a/R/alevin.R b/R/alevin.R
@@ -75,12 +75,12 @@ readAlevin <- function(files, dropInfReps, forceSlow) {
   if (!requireNamespace("fishpond", quietly=TRUE)) {
     hasFishpond <- FALSE
   } else {
-    if (packageVersion("fishpond") < "1.1.17") {
+    if (packageVersion("fishpond") < "1.1.18") {
       hasFishpond <- FALSE
     }
   }
   if (!hasFishpond)
-    message("importing alevin data is much faster after installing `fishpond` (>= 1.1.17)")
+    message("importing alevin data is much faster after installing `fishpond` (>= 1.1.18)")
 
   # for testing purposes, force the use of the slower R code for importing alevin
   if (forceSlow) {
@@ -204,22 +204,8 @@ readAlevinBits <- function(matrix.file, gene.names, cell.names) {
 readAlevinFast <- function(matrix.file, gene.names, cell.names) {
   num.cells <- length(cell.names)
   num.genes <- length(gene.names)
-
-  dat <- fishpond::readEDS(matrix.file, num.genes, num.cells)
-
-  # `dat$pos + 1` is `gene.idx` in the readAlevinBits() function
-  len.gene.idx <- lengths(dat$pos)
-  cell.idx <- rep(seq_along(len.gene.idx), len.gene.idx)
-
-  # build sparse matrix
-  # Note! we add 1 to the 0-based positions returned from fishpond::readEDS()
-  gene.idx <- unlist(dat$pos) + 1
-  mat <- Matrix::sparseMatrix(i=gene.idx,
-                              j=cell.idx,
-                              x=unlist(dat$exp),
-                              dims=c(num.genes, num.cells),
-                              dimnames=list(gene.names, cell.names),
-                              giveCsparse=FALSE)
+  mat <- fishpond::readEDS(num.genes, num.cells, matrix.file)
+  dimnames(mat) <- list(gene.names, cell.names)
   mat
 }
 

diff --git a/tests/testthat/test_alevin.R b/tests/testthat/test_alevin.R
@@ -7,6 +7,7 @@ test_that("import alevin works", {
 
   txi <- tximport(files, type="alevin")
 
+  dir <- system.file("extdata", package="tximportData")
   files <- file.path(dir,"alevin/neurons_900_v014/alevin/quants_mat.gz")
   file.exists(files)