@@ -1,3 +1,4 @@

+

 % \VignetteIndexEntry{gmapR}

 % \VignetteKeywords{gmap,gsnap}

 % \VignettePackage{gmapR}

@@ -256,9 +257,9 @@ bam_file <- file.path(system.file(package = "gmapR", mustWork=TRUE),

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

 bqual <- 56L

 mapq <- 13L

-param <- BamTallyParam(cycle_breaks = as.integer(breaks),

-                       high_quality_cutoff = as.integer(bqual),

-                       minimum_mapq = as.integer(mapq),

+param <- BamTallyParam(genome, cycle_breaks = breaks,

+                       high_quality_cutoff = bqual,

+                       minimum_mapq = mapq,

                        concordant_only = FALSE, unique_only = FALSE,

                        primary_only = FALSE,

                        min_depth = 0L, variant_strand = 1L,

@@ -266,7 +267,6 @@ param <- BamTallyParam(cycle_breaks = as.integer(breaks),

                        indels = FALSE)

 tallies <-bam_tally(bam_file,

-                    genome,

                     param)

 @