@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     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: 1.1.10

+Version: 1.1.11

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -2,7 +2,7 @@ test_snps <- function() {

   ## FIXME: rewrite this test to use the output of bam_tally, once we

   ## can convert those results to a VCF.

   library(gmapR)

-  genome <- GmapGenome("hg19_IGIS21", create = TRUE)

+  genome <- GmapGenome("hg19_IGIS21", create = TRUE, k = 12)

   dir <- GmapSnpDirectory(genome)

   gr <- as(seqinfo(genome), "GenomicRanges")

   gr <- GRanges("3", IRanges(3e6,4e6))

@@ -28,6 +28,8 @@ test_bam_tally_C <- function() {

   which <- RangesList("1" = IRanges(1e6, 2e6))

   bam <- "~/share/data/R1047_LIB6635_SAM636095_L1_NXG2449.analyzed.bam"

   bf <- Rsamtools::BamFile(bam)

-  gr <- bam_tally(bf, BamTallyParam(genome, which = which, variant_strand = 1L))

+  gr <- bam_tally(bf, BamTallyParam(genome, which = which, variant_strand = 1L,

+                                    cycle_breaks = c(0L, 10L, 75L),

+                                    indels = TRUE))

 }

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

 test_GmapGenome_constructor_DNAStringSet_noCreate <- function() {

   dna <- Biostrings::DNAStringSet("ACTGTGTCAG")

   names(dna) <- "test"

-  gmapGenome <- GmapGenome(genome=dna, name="thing", create=FALSE)

+  gmapGenome <- GmapGenome(genome=dna, name="thing", create=FALSE, k = 12)

   checkTrue(is(gmapGenome, "GmapGenome"))

 }

@@ -15,10 +15,10 @@ test_GmapGenome_constructor_DNAStringSet_create <- function() {

   dir.create(genomeDir, recursive=TRUE)

   on.exit(unlink(genomeDir, recursive=TRUE))

   checkException(GmapGenome(genome=dna, directory=genomeDir,

-                            name="thing", create=TRUE))

+                            name="thing", create=TRUE, k=12))

   names(dna) <- "sampleDNAStringSet"

   gmapGenome <- GmapGenome(genome=dna, directory=genomeDir,

-                           name="thing", create=TRUE)

+                           name="thing", create=TRUE, k=12)

   checkTrue(is(gmapGenome, "GmapGenome"))

 }

@@ -30,14 +30,14 @@ test_GmapGenome_constructor_BSgenome_create <- function() {

   dir.create(genomeDir, recursive=TRUE)  

   on.exit(unlink(genomeDir, recursive=TRUE))

   gmapGenome <- GmapGenome(genome=Scerevisiae, directory=genomeDir,

-                           name=genomeName, create=TRUE)                           

+                           name=genomeName, create=TRUE, k=12) 

   checkTrue(is(gmapGenome, "GmapGenome"))

 }

 testGmapGenome_constructor_FastaFile_create <- function() {

   fa <- system.file("extdata/hg19.p53.fasta", package="gmapR", mustWork=TRUE)

   fastaFile <- rtracklayer::FastaFile(fa)

-  gmapGenome <- GmapGenome(fastaFile, create=TRUE)

+  gmapGenome <- GmapGenome(fastaFile, create=TRUE, k=12)

   checkTrue(is(gmapGenome, "GmapGenome"))

 }

@@ -50,7 +50,7 @@ test_GmapGenome_accessors <- function() {

   dir.create(genomeDir, recursive=TRUE)

   on.exit(unlink(genomeDir, recursive=TRUE))

   gmapGenome <- GmapGenome(genome=dna, directory=genomeDir,

-                           name=genomeName, create=FALSE)

+                           name=genomeName, create=FALSE, k=12)

   checkIdentical(path(gmapGenome), file.path(genomeDir, genomeName))

   checkTrue(is(directory(gmapGenome), "GmapGenomeDirectory"))

   checkIdentical(genome(gmapGenome), genomeName)

@@ -2,7 +2,7 @@ test_GsnapParam_constructor <- function() {

   fa <- system.file("extdata/hg19.p53.fasta", package="gmapR", mustWork=TRUE)

   fastaFile <- rtracklayer::FastaFile(fa)

-  gmapGenome <- GmapGenome(fastaFile, create=TRUE)

+  gmapGenome <- GmapGenome(fastaFile, create=TRUE, k = 12)

   gsnapParam <- GsnapParam(genome = gmapGenome,

                            unique_only = FALSE,

@@ -8,7 +8,8 @@ test_makeGmapGenomePackage_sacCer3 <- function() {

   gmapGenome <- GmapGenome(genome=Scerevisiae,

                            directory = ggd,

                            name = "yeast",

-                           create = TRUE)

+                           create = TRUE,

+                           k = 12)

   packageDestDir <- file.path(tempdir(), as.integer(runif(1) * 100000))

   on.exit(unlink(packageDestDir, recursive=TRUE), add=TRUE)