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

 Package: SplicingGraphs

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

 	to them

-Version: 1.5.1

+Version: 1.5.2

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

 License: Artistic-2.0

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

@@ -11,8 +11,8 @@ Description: This package allows the user to create, manipulate, and visualize

         different ways.

 Maintainer: H. Pages <[email protected]>

 Depends: BiocGenerics,

-	 S4Vectors (>= 0.0.1), IRanges (>= 1.99.1), GenomicRanges (>= 1.17.7),

-	 GenomicFeatures (>= 1.17.3), GenomicAlignments (>= 1.1.4),

+	 S4Vectors (>= 0.1.0), IRanges (>= 1.99.21), GenomicRanges (>= 1.17.22),

+	 GenomicFeatures (>= 1.17.3), GenomicAlignments (>= 1.1.22),

 	 Rgraphviz (>= 2.3.7)

 Imports: methods, utils, igraph,

 	 BiocGenerics,

@@ -118,7 +118,7 @@ assignReads <- function(sg, reads, sample.name=NA)

     } else {

         ## Paired-end reads. We produce a GRangesList object with 2 ranges

         ## per top-level elements.

-        reads2 <- GenomicRanges:::fillGaps(reads)

+        reads2 <- GenomicAlignments:::fillJunctionGaps(reads)

     }

     sg@genes@unlistData <- .assignSubfeatureHits(reads2, ex_by_tx, ov1,

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

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

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

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

 %\VignetteKeywords{Annotation}

 %\VignettePackage{SplicingGraphs}

 \documentclass{article}

@@ -825,7 +825,7 @@ package:

 <<quickBamFlagSummary>>=

 library(Rsamtools)

-quickBamFlagSummary(bam_files[1], mainGroupsOnly=TRUE)

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

 @

 Doing this for the 8 BAM files confirms that all the reads in the

@@ -855,9 +855,9 @@ records won't be paired and will be returned in a \Rclass{GAlignments} object.

 We can use the \Rcode{assignReads} function to assign reads to the

 the exonic and intronic edges of \Rcode{sg}. The same read

 can be assigned to more than one exonic or intronic edge. For example,

-a junction read with 1 gap (i.e., 1 \Rcode{N} in its CIGAR) can be assigned

-to an intron and its 2 flanking exons, and this can happen for one or more

-transcripts, from the same gene or from different genes.

+a junction read with 1 junction (i.e., 1 \Rcode{N} in its CIGAR) can be

+assigned to an intron and its 2 flanking exons, and this can happen for

+one or more transcripts, from the same gene or from different genes.

 We're going to loop on the BAM files to assign the reads from 1 run

 at a time. When we load the files, we want to filter out secondary

@@ -928,25 +928,25 @@ head(edge_data[ , c("sgedge_id", "ERR127306.hits")])

 For the purpose of explaining how reads from run \Rcode{ERR127306}

 were assigned to the edges of gene 3183, we load the reads that are

-in the region of that gene and have at least 1 gap:

+in the region of that gene and contain at least 1 junction:

 <<load_reads_in_3183_region>>=

 param <- ScanBamParam(flag=flag0, which=range(unlist(sg[["3183"]])))

 reads <- readGAlignmentPairs(bam_files[1], use.names=TRUE, param=param)

-gapped_reads <- reads[njunc(first(reads)) + njunc(last(reads)) != 0L]

+junction_reads <- reads[njunc(first(reads)) + njunc(last(reads)) != 0L]

 @

 and we plot the genomic region chr14:21675000-21702000:

 <<plotTranscripts_sg_3183_and_reads,eval=FALSE>>=

-plotTranscripts(sg[["3183"]], reads=gapped_reads, from=21675000, to=21702000)

+plotTranscripts(sg[["3183"]], reads=junction_reads, from=21675000, to=21702000)

 @

 The resulting plot is shown on figure \ref{img:3183-transcripts-and-reads}.

 <<plotTranscripts_sg_3183_and_reads_as_pdf,echo=FALSE,results=hide>>=

 pdf("3183-transcripts-and-reads.pdf", width=12, height=12)

-plotTranscripts(sg[["3183"]], reads=gapped_reads, from=21675000, to=21702000)

+plotTranscripts(sg[["3183"]], reads=junction_reads, from=21675000, to=21702000)

 dev.off()

 @

 \begin{figure}[!htbp]

@@ -965,12 +965,12 @@ Figure \ref{img:3183-transcripts-and-reads-zoom} is a zoom on genomic region

 chr14:21698400-21698600 that was obtained with:

 <<plotTranscripts_sg_3183_and_reads_zoom,eval=FALSE>>=

-plotTranscripts(sg[["3183"]], reads=gapped_reads, from=21698400, to=21698600)

+plotTranscripts(sg[["3183"]], reads=junction_reads, from=21698400, to=21698600)

 @

 <<plotTranscripts_sg_3183_and_reads_zoom_as_pdf,echo=FALSE,results=hide>>=

 pdf("3183-transcripts-and-reads-zoom.pdf", width=12, height=12)

-plotTranscripts(sg[["3183"]], reads=gapped_reads, from=21698400, to=21698600)

+plotTranscripts(sg[["3183"]], reads=junction_reads, from=21698400, to=21698600)

 dev.off()

 @

 \begin{figure}[!htbp]

Binary files a/vignettes/precomputed_results/sg_with_bubbles.rda and b/vignettes/precomputed_results/sg_with_bubbles.rda differ

Binary files a/vignettes/precomputed_results/sg_with_reads.rda and b/vignettes/precomputed_results/sg_with_reads.rda differ