Dropped rSFFreader package

malnirav · May 6, 2019 · 554758f · 554758f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: hiReadsProcessor
 Title: Functions to process LM-PCR reads from 454/Illumina data
-Version: 1.19.0
-Date: 2016-05-05
+Version: 1.19.1
+Date: 2019-05-07
 Author: Nirav V Malani <[email protected]>
 Maintainer: Nirav V Malani <[email protected]>
 Description: hiReadsProcessor contains set of functions which allow
@@ -22,7 +22,6 @@ Imports:
     dplyr,
     BiocGenerics,
     GenomicRanges,
-    rSFFreader,
     readxl,
     methods
 License: GPL-3
@@ -33,4 +32,4 @@ Suggests:
 biocViews: Sequencing, Preprocessing
 LazyLoad: yes
 SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT
-RoxygenNote: 5.0.1
+RoxygenNote: 6.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -71,8 +71,6 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
 importFrom(methods,as)
 importFrom(methods,is)
-importFrom(rSFFreader,readSff)
-importFrom(rSFFreader,sread)
 importFrom(readxl,read_excel)
 importFrom(stats,aggregate)
 importFrom(stats,ave)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN 1.19.1
+-----------------------
+
+    * Dropped rSFFreader dependency
+
 CHANGES IN 1.9.3
 -----------------------
 

diff --git a/R/hiReadsProcessor.R b/R/hiReadsProcessor.R
@@ -8,7 +8,6 @@
 #'
 #' @import BiocParallel Biostrings GenomicAlignments hiAnnotator 
 #' sonicLength BiocGenerics GenomicRanges
-#' @importFrom rSFFreader sread readSff
 #' @importFrom readxl read_excel
 #' @importFrom dplyr count arrange summarise rename mutate select ungroup
 #' group_by bind_rows left_join desc n %>% contains
@@ -86,7 +85,6 @@ NULL
 #' \dontrun{
 #' read.SeqFolder(".", seqfilePattern = "\\.TCA.454Reads.fna$")
 #' read.SeqFolder(".", seqfilePattern = ".+fastq$")
-#' read.SeqFolder(".", seqfilePattern = ".+sff$")
 #' }
 read.SeqFolder <- function(sequencingFolderPath = NULL, 
                            sampleInfoFilePath = NULL,
@@ -3914,11 +3912,11 @@ getSectorsForSamples <- function(sampleInfo, sector = NULL, samplename = NULL,
   }
 }
 
-#' Read fasta/fastq/sff given the path or sampleInfo object.
+#' Read fasta/fastq given the path or sampleInfo object.
 #'
 #' Given a sequence reads file path, the function returns a DNAStringSet object.
 #'
-#' @param seqFilePath a path to fasta/fastq/sff reads file or a sampleInfo 
+#' @param seqFilePath a path to fasta/fastq reads file or a sampleInfo 
 #' object returned by \code{\link{read.SeqFolder}}
 #' @param sector specific sector to reads sequences from. Default is 1, and not 
 #' required if seqFilePath is a direct file path rather than sampleInfo object.
@@ -4032,11 +4030,6 @@ read.seqsFromSector <- function(seqFilePath=NULL, sector=1, isPaired=FALSE) {
       ## for single-end data!
       dnaSet <- dnaSet[[1]]
     }
-  } else if (any(grepl("sff", seqFilePath, ignore.case = TRUE))) {    
-    dnaSet <- rSFFreader::sread(rSFFreader::readSff(seqFilePath,
-                                                    use.qualities = FALSE,
-                                                    verbose = FALSE))
-    doSingleEndCheck <- TRUE    
   } else {
     dnaSet <- readDNAStringSet(seqFilePath)
     doSingleEndCheck <- TRUE    

diff --git a/man/addFeature.Rd b/man/addFeature.Rd
diff --git a/man/addListNameToReads.Rd b/man/addListNameToReads.Rd
diff --git a/man/annotateSites.Rd b/man/annotateSites.Rd
diff --git a/man/blatListedSet.Rd b/man/blatListedSet.Rd
diff --git a/man/blatSeqs.Rd b/man/blatSeqs.Rd
diff --git a/man/chunkize.Rd b/man/chunkize.Rd
diff --git a/man/clusterSites.Rd b/man/clusterSites.Rd
diff --git a/man/crossOverCheck.Rd b/man/crossOverCheck.Rd
diff --git a/man/dereplicateReads.Rd b/man/dereplicateReads.Rd
diff --git a/man/doRCtest.Rd b/man/doRCtest.Rd
diff --git a/man/extractFeature.Rd b/man/extractFeature.Rd
diff --git a/man/extractSeqs.Rd b/man/extractSeqs.Rd
diff --git a/man/findAndRemoveVector.Rd b/man/findAndRemoveVector.Rd
diff --git a/man/findAndTrimSeq.Rd b/man/findAndTrimSeq.Rd
diff --git a/man/findBarcodes.Rd b/man/findBarcodes.Rd
diff --git a/man/findIntegrations.Rd b/man/findIntegrations.Rd
diff --git a/man/findLTRs.Rd b/man/findLTRs.Rd
diff --git a/man/findLinkers.Rd b/man/findLinkers.Rd
diff --git a/man/findPrimers.Rd b/man/findPrimers.Rd
diff --git a/man/findVector.Rd b/man/findVector.Rd
diff --git a/man/getIntegrationSites.Rd b/man/getIntegrationSites.Rd
diff --git a/man/getSectorsForSamples.Rd b/man/getSectorsForSamples.Rd
diff --git a/man/getSonicAbund.Rd b/man/getSonicAbund.Rd
diff --git a/man/hiReadsProcessor.Rd b/man/hiReadsProcessor.Rd
diff --git a/man/isuSites.Rd b/man/isuSites.Rd
diff --git a/man/otuSites.Rd b/man/otuSites.Rd
diff --git a/man/pairUpAlignments.Rd b/man/pairUpAlignments.Rd
diff --git a/man/pairwiseAlignSeqs.Rd b/man/pairwiseAlignSeqs.Rd
diff --git a/man/primerIDAlignSeqs.Rd b/man/primerIDAlignSeqs.Rd
diff --git a/man/psl.Rd b/man/psl.Rd