use readGAlignments() instead of readGAlignmentsFromBam()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPQC@98316 bc3139a8-67e5-0310-9ffc-ced21a209358
genialis · Jan 14, 2015 · e386fb8 · e386fb8
1 parent 303d488
commit e386fb8
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ChIPQC
 Type: Package
 Title: Quality metrics for ChIPseq data
-Version: 1.3.0
+Version: 1.3.1
 Date: 2014-05-12
 Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark
 Maintainer: Tom Carroll <[email protected]>, Rory Stark <[email protected]>

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,7 +11,7 @@ importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
 
 importMethodsFrom(BiocParallel, bplapply)
 
-importMethodsFrom(GenomicAlignments, readGAlignmentsFromBam)
+importMethodsFrom(GenomicAlignments, readGAlignments)
 
 importMethodsFrom(IRanges, as.list, as.matrix, "colnames<-",
                   countOverlaps, coverage, end, flank, gsub, mean, median,

diff --git a/R/sampleQC.R b/R/sampleQC.R
@@ -47,7 +47,7 @@ sampleQC <- function(bamFile,bedFile=NULL,blklist=NULL,ChrOfInterest=NULL,GeneAn
 
     Param <- ScanBamParam(which=GRanges(seqnames=names(ChrLengths)[k],IRanges(start=1,end=unname(ChrLengths[names(ChrLengths) == names(ChrLengths)[k]])-shiftWindowEnd)),
                           what=c("flag","mapq"))
-    temp <- readGAlignmentsFromBam(bamFile,param=Param)
+    temp <- readGAlignments(bamFile,param=Param)
     if(length(temp) < 1){
 
       emptyChr_SSD <- 0