@@ -9,10 +9,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.17.1

+Version: 1.17.2

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)

-Imports: S4Vectors (>= 0.9.25), IRanges, 

+Imports: S4Vectors (>= 0.13.13), IRanges, 

         rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,

         VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,

         GenomicAlignments (>= 1.1.9), BiocParallel

@@ -9,7 +9,7 @@

 setClass("BamTallyParam",

          representation(genome = "GmapGenome",

                         which = "GenomicRanges",

-                        desired_read_group = "characterORNULL",

+                        desired_read_group = "character_OR_NULL",

                         minimum_mapq = "integer",

                         concordant_only = "logical",

                         unique_only = "logical",

@@ -20,7 +20,7 @@ setClass("BamTallyParam",

                         ignore_query_Ns = "logical",

                         indels = "logical",

                         include_soft_clips = "integer",

-                        exon_iit = "characterORNULL",

+                        exon_iit = "character_OR_NULL",

                         xs = "logical",

                         read_pos = "logical",

                         min_base_quality = "integer",

@@ -7,8 +7,8 @@

 ### unique directory.

 ###

-setClassUnion("GmapParamORNULL", c("GmapParam", "NULL"))

-setIs("GmapParamORNULL", "GmapAlignerParamORNULL")

+setClassUnion("GmapParam_OR_NULL", c("GmapParam", "NULL"))

+setIs("GmapParam_OR_NULL", "GmapAlignerParam_OR_NULL")

 .valid_GmapOutput <- function(object) {

     if (length(paths(object)) == 0L)

@@ -17,8 +17,8 @@ setIs("GmapParamORNULL", "GmapAlignerParamORNULL")

 setClass("GmapOutput",

          representation(path = "character",

-                        param = "GmapParamORNULL",

-                        version = "POSIXltORNULL"),

+                        param = "GmapParam_OR_NULL",

+                        version = "POSIXlt_OR_NULL"),

          contains="GmapAlignerOutput",

          validity = .valid_GmapOutput)

@@ -5,13 +5,13 @@

 ### High-level interface to gmap.

 ###

-setClassUnion("GmapSnpsORNULL", c("GmapSnps", "NULL"))

+setClassUnion("GmapSnps_OR_NULL", c("GmapSnps", "NULL"))

 setClass("GmapAlignerParam",

          representation(genome = "GmapGenome",

-                        part = "characterORNULL",

+                        part = "character_OR_NULL",

                         batch = "character",

-                        snps = "GmapSnpsORNULL",

+                        snps = "GmapSnps_OR_NULL",

                         mode = "character",

                         nthreads = "integer",

                         npaths = "integer",

@@ -7,25 +7,25 @@

 ### unique directory.

 ###

-setClassUnion("POSIXltORNULL", c("POSIXlt", "NULL"))

+setClassUnion("POSIXlt_OR_NULL", c("POSIXlt", "NULL"))

 .valid_GsnapOutput <- function(object) {

   if (length(samPaths(object)) == 0L && length(bamPaths(object)) == 0L)

     paste0("No GSNAP output at '", object@path, "'")

 }

-setClassUnion("GmapAlignerParamORNULL", c("GmapAlignerParam", "NULL"))

+setClassUnion("GmapAlignerParam_OR_NULL", c("GmapAlignerParam", "NULL"))

-setClassUnion("GsnapParamORNULL", c("GsnapParam", "NULL"))

-setIs("GsnapParamORNULL", "GmapAlignerParamORNULL")

+setClassUnion("GsnapParam_OR_NULL", c("GsnapParam", "NULL"))

+setIs("GsnapParam_OR_NULL", "GmapAlignerParam_OR_NULL")

 setClass("GmapAlignerOutput",

          representation(path = "character",

-                        param = "GmapAlignerParamORNULL",

-                        version = "POSIXltORNULL"))

+                        param = "GmapAlignerParam_OR_NULL",

+                        version = "POSIXlt_OR_NULL"))

 setClass("GsnapOutput",

-         representation(param = "GsnapParamORNULL"),

+         representation(param = "GsnapParam_OR_NULL"),

          contains="GmapAlignerOutput",

          validity = .valid_GsnapOutput)

@@ -114,7 +114,7 @@ setMethod("bamPaths", "GmapAlignerOutput", function(x) {

 newGmapAlignerOutput <- function(Class, path, param = NULL, version = NULL) {

     if (!is.character(path) || any(is.na(path)))

         stop("'path' must be a character vector without any NA's")

-    if (!is(version, "POSIXltORNULL")) {

+    if (!is(version, "POSIXlt_OR_NULL")) {

         if (is.character(version))

             version <- parseGsnapVersion(version)

         else stop("'version' must be a version string, POSIXlt object or NULL")

@@ -8,13 +8,13 @@

 ### list.

 ###

-setClassUnion("integerORNULL", c("integer", "NULL"))

+setClassUnion("integer_OR_NULL", c("integer", "NULL"))

 setClass("GsnapParam",

-         representation(max_mismatches = "integerORNULL",

+         representation(max_mismatches = "integer_OR_NULL",

                         suboptimal_levels = "integer",

                         novelsplicing = "logical",

-                        splicing = "characterORNULL",

+                        splicing = "character_OR_NULL",

                         terminal_threshold = "integer",

                         gmap_mode = "character",

                         clip_overlap = "logical"),

@@ -205,12 +205,12 @@ setAs("GsnapParam", "list", function(from) {

 as.list.GmapAlignerParam <- function(x, ...) as(x, "list")

-setAs("ANY", "characterORNULL", function(from) {

+setAs("ANY", "character_OR_NULL", function(from) {

   if (is.null(from))

     NULL

   else as.character(from)

 })

-setAs("ANY", "integerORNULL", function(from) {

+setAs("ANY", "integer_OR_NULL", function(from) {

   if (is.null(from))

     NULL

   else as.integer(from)

@@ -9,7 +9,7 @@

 setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)

            standardGeneric("gsnap"))

-setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

+setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),

           function(input_a, input_b, params,

                    output = file.path(getwd(),

                      file_path_sans_ext(basename(input_a), TRUE)),

@@ -11,10 +11,10 @@

 ###

 setClass("IIT", representation(ptr = "externalptr"))

-setClassUnion("IITORNULL", c("IIT", "NULL"))

+setClassUnion("IIT_OR_NULL", c("IIT", "NULL"))

 setRefClass("IITFile",

-            fields=c(iit="IITORNULL"),

+            fields=c(iit="IIT_OR_NULL"),

             contains="RTLFile")

 IITFile <- function(resource) {

@@ -1,7 +1,7 @@

 \name{gsnap-methods}

 \docType{methods}

 \alias{gsnap-methods}

-\alias{gsnap,character,characterORNULL,GsnapParam-method}

+\alias{gsnap,character,character_OR_NULL,GsnapParam-method}

 \alias{gsnap}

 \title{Align a Set of Reads Using the GSNAP Aligner}

@@ -15,7 +15,7 @@

 }

 \usage{

-\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,

+\S4method{gsnap}{character,character_OR_NULL,GsnapParam}(input_a, input_b, params,

                    output = file.path(getwd(),

                                       file_path_sans_ext(basename(input_a),

                                                          TRUE)),