sync from bioconductor dev svn

.BBSoptions

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+UnsupportedPlatforms: win

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -1,22 +1,36 @@
 Package: hiReadsProcessor
-Title: Functions to process LM-PCR reads from 454/Illumina data.
-Version: 1.3.0
-Date: 2015-04-02
+Title: Functions to process LM-PCR reads from 454/Illumina data
+Version: 1.13.0
+Date: 2016-05-05
 Author: Nirav V Malani <[email protected]>
 Maintainer: Nirav V Malani <[email protected]>
 Description: hiReadsProcessor contains set of functions which allow
-        users to process LM-PCR products sequenced using any platform.
-        Given an excel/txt file containing parameters for
-        demultiplexing and sample metadata, the functions automate
-        trimming of adaptors and identification of the genomic product.
-        Genomic products are further processed for QC and abundance
-        quantification.
-Depends: Biostrings, GenomicAlignments, xlsx, BiocParallel,
-        hiAnnotator, R (>= 3.0)
-Imports: sonicLength, plyr, GenomicRanges, BiocGenerics, rSFFreader
+    users to process LM-PCR products sequenced using any platform.
+    Given an excel/txt file containing parameters for
+    demultiplexing and sample metadata, the functions automate
+    trimming of adaptors and identification of the genomic product.
+    Genomic products are further processed for QC and abundance
+    quantification.
+Depends:
+    Biostrings,
+    GenomicAlignments,
+    BiocParallel,
+    hiAnnotator,
+    R (>= 3.0)
+Imports:
+    sonicLength,
+    dplyr,
+    BiocGenerics,
+    GenomicRanges,
+    rSFFreader,
+    readxl,
+    methods
 License: GPL-3
 VignetteBuilder: knitr
-Suggests: knitr, testthat
+Suggests:
+    knitr,
+    testthat
 biocViews: Sequencing, Preprocessing
 LazyLoad: yes
-SystemRequirements: BLAT, JRE, UCSC hg18 in 2bit format for BLAT
+SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(addFeature)
 export(addListNameToReads)
@@ -48,15 +48,37 @@ export(troubleshootLinkers)
 export(vpairwiseAlignSeqs)
 export(write.listedDNAStringSet)
 export(write.psl)
+import(BiocGenerics)
 import(BiocParallel)
 import(Biostrings)
 import(GenomicAlignments)
+import(GenomicRanges)
 import(hiAnnotator)
-import(plyr)
 import(sonicLength)
-import(xlsx)
-import(GenomicRanges)
-import(BiocGenerics)
-importFrom(rSFFreader,sread)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,contains)
+importFrom(dplyr,count)
+importFrom(dplyr,desc)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+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)
+importFrom(stats,filter)
+importFrom(stats,na.omit)
+importFrom(stats,runif)
+importFrom(utils,count.fields)
+importFrom(utils,read.delim)
+importFrom(utils,write.table)

NEWS

@@ -1,17 +1,41 @@
-hiReadsProcessor News
+CHANGES IN 1.9.3
+-----------------------
+
+    * Namespace fixes for base R packages to alleviate build errors
+    * Updated findOverlap calls to use the new drop.self & drop.redundant args
+
+CHANGES IN 1.9.1
+-----------------------
+
+    * Using readxl to import sampleInfo excel file
+    * Minor code improvements for merging internal objects and cleaning data
+    * Removed parameter interactive in read.SeqFolder in favor of base::interactive()
+    * findOverlap calls updated to use ignoreRedundant & ignoreSelf
+    * splitSeqsToFiles receives outDir parameter
+
+CHANGES IN 1.4.0
+-----------------------
+
+    * Using dplyr for small computations
+
+CHANGES IN 1.1.3
+-----------------------
 
-CHANGES IN 1.1.3:
   * Modified all bplapply calls
   * Moved BiocGenerics and rSFFreader to Imports
 
-CHANGES IN 0.99.0:
+CHANGES IN 0.99.0
+-----------------------
+
   * Added examples for almost all functions
   * Removed Subread support
 
-CHANGES IN 0.3.35:
+CHANGES IN 0.3.35
+-----------------------
+
   * Added annotateSites
 
-CHANGES IN 0.3.34:
-  * bug fix dereplicateReads & write.psl
+CHANGES IN 0.3.34
+-----------------------
 
-INITIALIZATION 0.3.33
+  * Bug fix dereplicateReads & write.psl