fixed issues with bioparallel

vivekbhr · May 28, 2018 · 68579bf · 68579bf
1 parent 551bb72
commit 68579bf
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Showing 5 changed files with 16 additions and 16 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,7 +20,7 @@ Imports:
     ggplot2,
     GenomicFeatures,
     ShortRead,
-    BiocParallel,
+    BiocParallel (>= 1.15),
     Biostrings,
     S4Vectors,
     Rsamtools,

diff --git a/R/demultiplexFASTQ.R b/R/demultiplexFASTQ.R
@@ -191,14 +191,14 @@ setMethod("demultiplexFASTQ",
         ## get the fastq to split (raise error if fastq untrimmed/not existing)
         fastq_R1 <- CSobject@fastq_R1
         fastq_R2 <- CSobject@fastq_R2
-        param <- getMCparams(ncores)
-        message("de-multiplexing the FASTQ file")
+
         # register parallel backend
-        if (!BiocParallel::bpisup()) {
-        BiocParallel::bpstart()
-        on.exit(BiocParallel::bpstop())
+        param <- getMCparams(ncores)
+        if (!BiocParallel::bpisup(param)) {
+        BiocParallel::bpstart(param)
+        on.exit(BiocParallel::bpstop(param))
         }
-
+        message("de-multiplexing the FASTQ file")
         ## filter and write
         info <-
             BiocParallel::bplapply(seq_along(destinations), function(i) {

diff --git a/R/filterDuplicates.R b/R/filterDuplicates.R
@@ -135,9 +135,9 @@ setMethod("filterDuplicates",
     # run the filter duplicates function on all files
     bpParams <- getMCparams(ncores)
     # register parallel backend
-    if (!BiocParallel::bpisup()) {
-        BiocParallel::bpstart()
-        on.exit(BiocParallel::bpstop())
+    if (!BiocParallel::bpisup(bpParams)) {
+        BiocParallel::bpstart(bpParams)
+        on.exit(BiocParallel::bpstop(bpParams))
     }
 
     BiocParallel::bplapply(seq_along(bamfiles),

diff --git a/R/splitBAM_byIndex.R b/R/splitBAM_byIndex.R
@@ -73,9 +73,9 @@ splitBAM_byIndex <-
 
         param <- getMCparams(ncores)
         # register parallel backend
-        if (!BiocParallel::bpisup()) {
-            BiocParallel::bpstart()
-            on.exit(BiocParallel::bpstop())
+        if (!BiocParallel::bpisup(param)) {
+            BiocParallel::bpstart(param)
+            on.exit(BiocParallel::bpstop(param))
         }
         BiocParallel::bplapply(seq_along(destinations),
                                 function(i, file, destinations, filtrules) {

diff --git a/R/splitBAM_byRepindex.R b/R/splitBAM_byRepindex.R
@@ -62,9 +62,9 @@ splitBAM_byRepindex <-
 
         param <- getMCparams(ncores)
         # register parallel backend
-        if (!BiocParallel::bpisup()) {
-            BiocParallel::bpstart()
-            on.exit(BiocParallel::bpstop())
+        if (!BiocParallel::bpisup(param)) {
+            BiocParallel::bpstart(param)
+            on.exit(BiocParallel::bpstop(param))
         }
         BiocParallel::bplapply(seq_along(destinations),
                                function(i, file, destinations, filtrules) {