hg19 runvar bin bug for 1Mb

[Urja25]

Hi,

I noticed that when running runvarbin with Hg19 ref genome and 1Mb resolution, the function splits bins into 220kb size windows (as I get 12205 bins) at the end of this step. Here is an example:

tumor <- runVarbin("/path/to/clean_bam/", genome = "hg19", resolution = "1Mb", min_bincount = 10, remove_Y = FALSE, is_paired_end = TRUE)

tumor
class: CopyKit 
dim: 12205 7339 
metadata(3): genome resolution vst
assays(6): bincounts ft ... ratios logr
rownames(12205): 1 2 ... 12204 12205
rowData names(7): bin_length gene_count ... abspos arm
colnames(7339): AAACGAAAGATTAGAC-1.filtered.sorted AAACGAAAGCGTCAAG-1.filtered.sorted ...
  TTTGTGTTCGATAGCT-1.filtered.sorted TTTGTGTTCTACATCT-1.filtered.sorted
colData names(15): sample reads_assigned_bins ... cell_corr_value outlier
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowRanges has: 12205 ranges
Phylo: Phylogenetic tree with 0 tips and  nodes
consensus dim: 0 0

Could you please fix this in the source code?

Thanks!

[darlanminussi]

@Kris69w Could you take a look at this?

[Kris69w]

Hi, right now different genome resolution is only available for the hg38 genome. we will work on adding genome resolution scaffold other than 220kb for hg19.
Thanks!