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

 Package: SplicingGraphs

 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

 	to them

-Version: 1.7.3

+Version: 1.7.4

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages

 License: Artistic-2.0

 Description: This package allows the user to create, manipulate, and visualize

@@ -14,8 +14,8 @@ Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),

 	 Rgraphviz (>= 2.3.7)

 Imports: methods, utils, igraph,

 	 BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,

-	 GenomicFeatures, GenomicAlignments, graph, Rgraphviz

-Suggests: igraph, Gviz, Rsamtools (>= 1.19.17),

+	 GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz

+Suggests: igraph, Gviz,

 	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,

 	 RUnit

 Collate: utils.R

@@ -11,6 +11,7 @@ import(IRanges)

 import(GenomeInfoDb)

 import(GenomicRanges)

 import(GenomicFeatures)

+importFrom(Rsamtools, asBam)

 import(GenomicAlignments)

 importFrom(graph, nodeDataDefaults, nodeData,

@@ -18,10 +18,6 @@ toy_reads_sam <- function()

 toy_reads_bam <- function()

 {

-    ## The Rsamtools package is needed for asBam().

-    if (!requireNamespace("Rsamtools", quietly=TRUE))

-        stop("Couldn't load the Rsamtools package. Please install ",

-             "the Rsamtools\n  package and try again.")

     toy_reads_bam <- try(get("toy_reads_bam", envir=.toy_reads_bam_cache,

                              inherits=FALSE), silent=TRUE)

     if (!is(toy_reads_bam, "try-error"))

@@ -13,7 +13,6 @@

 .load_toy_reads <- function()

 {

-    library(Rsamtools)

     flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

@@ -37,6 +37,8 @@

 }

 \usage{

+## Constructor:

+

 SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)

 ## SplicingGraphs basic API:

@@ -75,7 +75,6 @@ removeReads(sg)

   when preparing the \link[Rsamtools]{ScanBamParam} object used to load

   the reads. For example:

   \preformatted{

-    library(Rsamtools)

     flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                          isNotPassingQualityControls=FALSE,

                          isDuplicate=FALSE)

@@ -143,7 +142,6 @@ names(sg)

 ## alignments, reads not passing quality controls, and PCR or optical

 ## duplicates (see ?scanBamFlag in the Rsamtools package for more

 ## information):

-library(Rsamtools)

 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                      isNotPassingQualityControls=FALSE,

                      isDuplicate=FALSE)

@@ -145,7 +145,6 @@ plot(sgraph(sg["geneD"], tx_id.as.edge.label=TRUE, as.igraph=TRUE))

 ## secondary alignments, reads not passing quality controls, and PCR or

 ## optical duplicates (see ?scanBamFlag in the Rsamtools package for

 ## more information):

-library(Rsamtools)

 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,

                      isNotPassingQualityControls=FALSE,

                      isDuplicate=FALSE)

@@ -1,5 +1,5 @@

 %\VignetteIndexEntry{Splicing graphs and RNA-seq data}

-%\VignetteDepends{SplicingGraphs,TxDb.Hsapiens.UCSC.hg19.knownGene,RNAseqData.HNRNPC.bam.chr14,Rsamtools,GenomicAlignments,Gviz}

+%\VignetteDepends{SplicingGraphs,TxDb.Hsapiens.UCSC.hg19.knownGene,RNAseqData.HNRNPC.bam.chr14,Gviz}

 %\VignetteKeywords{Annotation}

 %\VignettePackage{SplicingGraphs}

 \documentclass{article}

@@ -39,7 +39,7 @@

   Marc Carlson\and

   Martin Morgan}

-\date{Last modified: July 2014; Compiled: \today}

+\date{Last modified: January 2015; Compiled: \today}

 \begin{document}

@@ -822,7 +822,6 @@ single- or paired-end. This can be checked with the

 package:

 <<quickBamFlagSummary>>=

-library(Rsamtools)

 quickBamFlagSummary(bam_files[1], main.groups.only=TRUE)

 @

@@ -833,7 +832,6 @@ package. As a quick example, we load the reads located on the first 20

 million bases of chromosome 14:

 <<readGAlignmentPairs>>=

-library(GenomicAlignments)

 param <- ScanBamParam(which=GRanges("chr14", IRanges(1, 20000000)))

 galp <- readGAlignmentPairs(bam_files[1], param=param)

 length(galp)  # nb of alignment pairs

@@ -862,8 +860,8 @@ at a time. When we load the files, we want to filter out secondary

 alignments, reads not passing quality controls, and PCR or optical

 duplicates. This is done by preparing a \Rclass{ScanBamParam} object

 that we'll pass to \Rfunction{readGAlignmentPairs} (see

-\Rfunction{ScanBamParam} in the Rsamtools package for more information

-about this):

+\Rfunction{ScanBamParam} in the \Rpackage{Rsamtools} package for more

+information about this):

 <<ScanBamParam>>=

 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,