@@ -10,7 +10,7 @@ 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: 1.5.11

+Version: 1.5.12

 Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),

         GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4),

@@ -7,6 +7,7 @@ importFrom(Biobase, createPackage)

 import(IRanges)

 import(methods)

 import(GenomicRanges)

+importFrom(utils, packageVersion)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

 importFrom(GenomicRanges, genome, seqinfo)

 importMethodsFrom(GenomicRanges, seqnames, strand)

@@ -1,6 +1,10 @@

+geneGenomeName <- function(gene) {

+  paste0(gene, "_demo_", packageVersion("TxDb.Hsapiens.UCSC.hg19.knownGene"))

+}

+

 TP53Genome <- function() {

   gene <- "TP53"

-  genomeName <- paste0(gene, "_demo")

+  genomeName <- geneGenomeName(gene)

   if (genomeName %in% genome(GmapGenomeDirectory(create=TRUE))) {

     GmapGenome(genomeName)

@@ -58,7 +62,7 @@ translateToP53Genome <- function(x) {

   orgdb <- org.Hs.eg.db::org.Hs.eg.db

   roi <- getGeneRoi(txdb, orgdb, "TP53")

   subregion <- subsetRegion(x, roi, gene)

-  genome(subregion) <- "TP53_demo"

+  genome(subregion) <- geneGenomeName("TP53")

   subregion

 }

@@ -19,7 +19,9 @@ TP53Which()

   For \code{TP53Genome}, a \code{GmapGenome} object. If this is the

   first time the user has run this function, a side-effect will be the

   generation of an on-disk genome index, under the name

-  \dQuote{TP53_demo} in the default genome directory.

+  \dQuote{TP53_demo_VERSION} in the default genome directory, where

+  \code{VERSION} is the version of the TxDb package providing the bounds

+  of the P53 gene.

   For \code{TP53Which}, a \code{GRanges} of the extents of the TP53

   gene, translated to the space of \code{TP53Genome}.

@@ -182,9 +182,12 @@ library("gmapR")

 p53Seq <- getSeq(BSgenome.Hsapiens.UCSC.hg19::Hsapiens, roi,

                  as.character = FALSE) 

 names(p53Seq) <- "TP53"

-gmapGenome <- GmapGenome(genome = p53Seq, name = "TP53_demo", create = TRUE, 

+gmapGenome <- GmapGenome(genome = p53Seq, 

+                         name = paste0("TP53_demo_", 

+                           packageVersion("TxDb.Hsapiens.UCSC.hg19.knownGene")), 

+                         create = TRUE, 

                          k = 12L)

-@ 

+@

 We add the known transcripts (splice sites) to the genome index:

 <<set_TP53_splicesites>>=

@@ -294,11 +297,8 @@ summarizing these data into R data structures. For now, there is one:

 \Rfunction{variantSummary}, which returns a \Rcode{VRanges} object

 describing putative genetic variants in the sample.

 <<run_bamtally, eval=FALSE>>=

-library(gmapR)

-

 bam_file <- system.file("extdata/H1993.analyzed.bam", 

                         package="LungCancerLines", mustWork=TRUE)

-

 breaks <- c(0L, 15L, 60L, 75L)

 bqual <- 56L

 mapq <- 13L