tests/testthat/test-new_caller.R

In mskilab/loosends: Classifying loose ends in gGraphs

## library(loosends)

## tra.bp.gr.fn = system.file("extdata", "tests", "new_caller_1", "tra.bp.gr.rds", package = "loosends")
## tra.reads.dt.fn = system.file("extdata", "tests", "new_caller_1", "tra.reads.rds", package = "loosends")

## tra.bp.gr = readRDS(tra.bp.gr.fn)
## tra.reads.dt = readRDS(tra.reads.dt.fn)

## concat.fasta.fn = system.file("extdata", "hg19_loosends", "concatenated_references_deduped.fasta", package = "loosends")
## human.fasta.fn = system.file("extdata", "hg19_loosends", "human_g1k_v37_decoy.fasta", package = "loosends")
## concat = BWA(fasta = concat.fasta.fn)
## human = BWA(fasta = human.fasta.fn)

## ## TODO: STASH THIS
## dj = readRDS("~/projects/gGnome/files/zc_stash/unmappable.genome.rds")

## test_that(desc = "test new caller wrapper", code = {
##     suppressWarnings(
##         expr = {
##             res = call_loose_end2(li = tra.bp.gr,
##                                   ri = tra.reads.dt,
##                                   id = "387",
##                                   concat.bwa = concat,
##                                   human.bwa = human,
##                                   unmappable.gr = dj,
##                                   unmappable.pad = 5e3,
##                                   window = 1000,
##                                   verbose = FALSE)
##         })
## })